Starting phenix.real_space_refine on Fri Feb 6 00:54:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ook_70664/02_2026/9ook_70664.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ook_70664/02_2026/9ook_70664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ook_70664/02_2026/9ook_70664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ook_70664/02_2026/9ook_70664.map" model { file = "/net/cci-nas-00/data/ceres_data/9ook_70664/02_2026/9ook_70664.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ook_70664/02_2026/9ook_70664.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 13098 2.51 5 N 3411 2.21 5 O 4296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20928 Number of models: 1 Model: "" Number of chains: 57 Chain: "H" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1031 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 101} Chain: "f" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3525 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "g" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1026 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "I" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1031 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "M" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 101} Chain: "h" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3525 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "i" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1026 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "J" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1031 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "N" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 101} Chain: "j" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3525 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "k" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1026 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "g" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "i" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "k" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.83, per 1000 atoms: 0.23 Number of scatterers: 20928 At special positions: 0 Unit cell: (133.65, 133.65, 157.575, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 123 16.00 O 4296 8.00 N 3411 7.00 C 13098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Simple disulfide: pdb=" SG CYS f 54 " - pdb=" SG CYS f 74 " distance=2.04 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 205 " distance=2.03 Simple disulfide: pdb=" SG CYS f 126 " - pdb=" SG CYS f 196 " distance=2.04 Simple disulfide: pdb=" SG CYS f 131 " - pdb=" SG CYS f 157 " distance=2.03 Simple disulfide: pdb=" SG CYS f 201 " - pdb=" SG CYS f 433 " distance=2.03 Simple disulfide: pdb=" SG CYS f 218 " - pdb=" SG CYS f 247 " distance=2.03 Simple disulfide: pdb=" SG CYS f 228 " - pdb=" SG CYS f 239 " distance=2.03 Simple disulfide: pdb=" SG CYS f 296 " - pdb=" SG CYS f 331 " distance=2.03 Simple disulfide: pdb=" SG CYS f 378 " - pdb=" SG CYS f 445 " distance=2.02 Simple disulfide: pdb=" SG CYS f 385 " - pdb=" SG CYS f 418 " distance=2.03 Simple disulfide: pdb=" SG CYS f 501 " - pdb=" SG CYS g 605 " distance=2.03 Simple disulfide: pdb=" SG CYS g 598 " - pdb=" SG CYS g 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 104 " distance=2.03 Simple disulfide: pdb=" SG CYS h 54 " - pdb=" SG CYS h 74 " distance=2.04 Simple disulfide: pdb=" SG CYS h 119 " - pdb=" SG CYS h 205 " distance=2.03 Simple disulfide: pdb=" SG CYS h 126 " - pdb=" SG CYS h 196 " distance=2.03 Simple disulfide: pdb=" SG CYS h 131 " - pdb=" SG CYS h 157 " distance=2.03 Simple disulfide: pdb=" SG CYS h 201 " - pdb=" SG CYS h 433 " distance=2.03 Simple disulfide: pdb=" SG CYS h 218 " - pdb=" SG CYS h 247 " distance=2.03 Simple disulfide: pdb=" SG CYS h 228 " - pdb=" SG CYS h 239 " distance=2.03 Simple disulfide: pdb=" SG CYS h 296 " - pdb=" SG CYS h 331 " distance=2.03 Simple disulfide: pdb=" SG CYS h 378 " - pdb=" SG CYS h 445 " distance=2.03 Simple disulfide: pdb=" SG CYS h 385 " - pdb=" SG CYS h 418 " distance=2.03 Simple disulfide: pdb=" SG CYS h 501 " - pdb=" SG CYS i 605 " distance=2.03 Simple disulfide: pdb=" SG CYS i 598 " - pdb=" SG CYS i 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS j 54 " - pdb=" SG CYS j 74 " distance=2.04 Simple disulfide: pdb=" SG CYS j 119 " - pdb=" SG CYS j 205 " distance=2.03 Simple disulfide: pdb=" SG CYS j 126 " - pdb=" SG CYS j 196 " distance=2.03 Simple disulfide: pdb=" SG CYS j 131 " - pdb=" SG CYS j 157 " distance=2.03 Simple disulfide: pdb=" SG CYS j 201 " - pdb=" SG CYS j 433 " distance=2.03 Simple disulfide: pdb=" SG CYS j 218 " - pdb=" SG CYS j 247 " distance=2.03 Simple disulfide: pdb=" SG CYS j 228 " - pdb=" SG CYS j 239 " distance=2.03 Simple disulfide: pdb=" SG CYS j 296 " - pdb=" SG CYS j 331 " distance=2.03 Simple disulfide: pdb=" SG CYS j 378 " - pdb=" SG CYS j 445 " distance=2.03 Simple disulfide: pdb=" SG CYS j 385 " - pdb=" SG CYS j 418 " distance=2.03 Simple disulfide: pdb=" SG CYS j 501 " - pdb=" SG CYS k 605 " distance=2.03 Simple disulfide: pdb=" SG CYS k 598 " - pdb=" SG CYS k 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA E 3 " - " MAN E 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA o 3 " - " MAN o 4 " " BMA q 3 " - " MAN q 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " " BMA E 3 " - " MAN E 5 " " BMA V 3 " - " MAN V 5 " " BMA X 3 " - " MAN X 5 " " BMA o 3 " - " MAN o 5 " " BMA q 3 " - " MAN q 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A 1 " - " ASN f 392 " " NAG B 1 " - " ASN f 332 " " NAG C 1 " - " ASN f 262 " " NAG D 1 " - " ASN f 156 " " NAG E 1 " - " ASN f 160 " " NAG F 1 " - " ASN f 197 " " NAG G 1 " - " ASN f 234 " " NAG K 1 " - " ASN f 241 " " NAG O 1 " - " ASN f 276 " " NAG P 1 " - " ASN f 301 " " NAG Q 1 " - " ASN f 448 " " NAG R 1 " - " ASN f 465 " " NAG S 1 " - " ASN f 363 " " NAG T 1 " - " ASN h 392 " " NAG U 1 " - " ASN h 332 " " NAG V 1 " - " ASN h 262 " " NAG W 1 " - " ASN h 156 " " NAG X 1 " - " ASN h 160 " " NAG Y 1 " - " ASN h 197 " " NAG Z 1 " - " ASN h 234 " " NAG a 1 " - " ASN h 241 " " NAG b 1 " - " ASN h 276 " " NAG c 1 " - " ASN h 301 " " NAG d 1 " - " ASN h 448 " " NAG e 1 " - " ASN h 465 " " NAG f 601 " - " ASN f 88 " " NAG f 602 " - " ASN f 133 " " NAG f 603 " - " ASN f 339 " " NAG f 604 " - " ASN f 355 " " NAG f 605 " - " ASN f 269 " " NAG f 606 " - " ASN f 398 " " NAG f 607 " - " ASN f 386 " " NAG g 701 " - " ASN g 611 " " NAG g 702 " - " ASN g 637 " " NAG g 703 " - " ASN g 625 " " NAG h 601 " - " ASN h 88 " " NAG h 602 " - " ASN h 133 " " NAG h 603 " - " ASN h 339 " " NAG h 604 " - " ASN h 355 " " NAG h 605 " - " ASN h 269 " " NAG h 606 " - " ASN h 398 " " NAG h 607 " - " ASN h 386 " " NAG i 701 " - " ASN i 611 " " NAG i 702 " - " ASN i 637 " " NAG i 703 " - " ASN i 625 " " NAG j 601 " - " ASN j 88 " " NAG j 602 " - " ASN j 133 " " NAG j 603 " - " ASN j 339 " " NAG j 604 " - " ASN j 355 " " NAG j 605 " - " ASN j 269 " " NAG j 606 " - " ASN j 398 " " NAG j 607 " - " ASN j 386 " " NAG k 701 " - " ASN k 611 " " NAG k 702 " - " ASN k 637 " " NAG k 703 " - " ASN k 625 " " NAG l 1 " - " ASN h 363 " " NAG m 1 " - " ASN j 392 " " NAG n 1 " - " ASN j 332 " " NAG o 1 " - " ASN j 262 " " NAG p 1 " - " ASN j 156 " " NAG q 1 " - " ASN j 160 " " NAG r 1 " - " ASN j 197 " " NAG s 1 " - " ASN j 234 " " NAG t 1 " - " ASN j 241 " " NAG u 1 " - " ASN j 276 " " NAG v 1 " - " ASN j 301 " " NAG w 1 " - " ASN j 448 " " NAG x 1 " - " ASN j 465 " " NAG y 1 " - " ASN j 363 " Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 834.0 milliseconds 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4494 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 47 sheets defined 17.9% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 52 through 55 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'f' and resid 99 through 117 Processing helix chain 'f' and resid 122 through 126 removed outlier: 4.191A pdb=" N CYS f 126 " --> pdb=" O THR f 123 " (cutoff:3.500A) Processing helix chain 'f' and resid 334 through 354 removed outlier: 3.868A pdb=" N THR f 351 " --> pdb=" O GLU f 347 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR f 352 " --> pdb=" O LYS f 348 " (cutoff:3.500A) Processing helix chain 'f' and resid 368 through 373 Processing helix chain 'f' and resid 475 through 481 removed outlier: 3.684A pdb=" N TRP f 479 " --> pdb=" O MET f 475 " (cutoff:3.500A) Processing helix chain 'g' and resid 529 through 534 removed outlier: 3.816A pdb=" N SER g 534 " --> pdb=" O MET g 530 " (cutoff:3.500A) Processing helix chain 'g' and resid 536 through 543 removed outlier: 3.984A pdb=" N GLN g 540 " --> pdb=" O THR g 536 " (cutoff:3.500A) Processing helix chain 'g' and resid 569 through 596 removed outlier: 4.029A pdb=" N LEU g 592 " --> pdb=" O ARG g 588 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU g 593 " --> pdb=" O ASP g 589 " (cutoff:3.500A) Processing helix chain 'g' and resid 620 through 626 Processing helix chain 'g' and resid 635 through 637 No H-bonds generated for 'chain 'g' and resid 635 through 637' Processing helix chain 'g' and resid 638 through 658 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'h' and resid 99 through 117 Processing helix chain 'h' and resid 122 through 126 removed outlier: 4.190A pdb=" N CYS h 126 " --> pdb=" O THR h 123 " (cutoff:3.500A) Processing helix chain 'h' and resid 334 through 354 removed outlier: 3.855A pdb=" N THR h 351 " --> pdb=" O GLU h 347 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR h 352 " --> pdb=" O LYS h 348 " (cutoff:3.500A) Processing helix chain 'h' and resid 368 through 373 Processing helix chain 'h' and resid 475 through 484 removed outlier: 3.676A pdb=" N GLU h 482 " --> pdb=" O ASN h 478 " (cutoff:3.500A) Processing helix chain 'i' and resid 529 through 534 removed outlier: 3.789A pdb=" N SER i 534 " --> pdb=" O MET i 530 " (cutoff:3.500A) Processing helix chain 'i' and resid 536 through 543 removed outlier: 3.988A pdb=" N GLN i 540 " --> pdb=" O THR i 536 " (cutoff:3.500A) Processing helix chain 'i' and resid 569 through 596 removed outlier: 4.031A pdb=" N LEU i 592 " --> pdb=" O ARG i 588 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU i 593 " --> pdb=" O ASP i 589 " (cutoff:3.500A) Processing helix chain 'i' and resid 620 through 626 Processing helix chain 'i' and resid 635 through 637 No H-bonds generated for 'chain 'i' and resid 635 through 637' Processing helix chain 'i' and resid 638 through 658 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'j' and resid 99 through 117 Processing helix chain 'j' and resid 122 through 126 removed outlier: 4.192A pdb=" N CYS j 126 " --> pdb=" O THR j 123 " (cutoff:3.500A) Processing helix chain 'j' and resid 334 through 354 removed outlier: 3.862A pdb=" N THR j 351 " --> pdb=" O GLU j 347 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR j 352 " --> pdb=" O LYS j 348 " (cutoff:3.500A) Processing helix chain 'j' and resid 368 through 373 Processing helix chain 'j' and resid 425 through 429 removed outlier: 4.078A pdb=" N GLN j 428 " --> pdb=" O ASN j 425 " (cutoff:3.500A) Processing helix chain 'j' and resid 476 through 481 Processing helix chain 'k' and resid 529 through 534 removed outlier: 3.791A pdb=" N SER k 534 " --> pdb=" O MET k 530 " (cutoff:3.500A) Processing helix chain 'k' and resid 536 through 543 removed outlier: 3.984A pdb=" N GLN k 540 " --> pdb=" O THR k 536 " (cutoff:3.500A) Processing helix chain 'k' and resid 569 through 596 removed outlier: 4.035A pdb=" N LEU k 592 " --> pdb=" O ARG k 588 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU k 593 " --> pdb=" O ASP k 589 " (cutoff:3.500A) Processing helix chain 'k' and resid 620 through 626 Processing helix chain 'k' and resid 635 through 637 No H-bonds generated for 'chain 'k' and resid 635 through 637' Processing helix chain 'k' and resid 638 through 658 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.526A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.526A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 45 through 51 removed outlier: 7.254A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 45 through 51 removed outlier: 7.254A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 100B through 100C Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.927A pdb=" N ILE L 54 " --> pdb=" O TRP L 41 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN L 43 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL L 52 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 494 through 499 removed outlier: 5.589A pdb=" N VAL g 608 " --> pdb=" O VAL f 36 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N VAL f 38 " --> pdb=" O THR g 606 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N THR g 606 " --> pdb=" O VAL f 38 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N TYR f 40 " --> pdb=" O CYS g 604 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N CYS g 604 " --> pdb=" O TYR f 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'f' and resid 45 through 47 Processing sheet with id=AB1, first strand: chain 'f' and resid 55 through 56 Processing sheet with id=AB2, first strand: chain 'f' and resid 66 through 67 removed outlier: 6.962A pdb=" N HIS f 66 " --> pdb=" O SER f 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'f' and resid 91 through 94 Processing sheet with id=AB4, first strand: chain 'f' and resid 181 through 183 Processing sheet with id=AB5, first strand: chain 'f' and resid 202 through 203 removed outlier: 6.297A pdb=" N THR f 202 " --> pdb=" O TYR f 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'f' and resid 259 through 261 removed outlier: 3.678A pdb=" N GLY f 451 " --> pdb=" O LEU f 260 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLY f 451 " --> pdb=" O GLN f 290 " (cutoff:3.500A) removed outlier: 10.691A pdb=" N GLN f 290 " --> pdb=" O GLY f 451 " (cutoff:3.500A) removed outlier: 12.167A pdb=" N LEU f 453 " --> pdb=" O LEU f 288 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N LEU f 288 " --> pdb=" O LEU f 453 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N THR f 455 " --> pdb=" O VAL f 286 " (cutoff:3.500A) removed outlier: 11.667A pdb=" N VAL f 286 " --> pdb=" O THR f 455 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS f 330 " --> pdb=" O ILE f 297 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE f 376 " --> pdb=" O PHE f 383 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'f' and resid 271 through 273 removed outlier: 3.582A pdb=" N THR f 271 " --> pdb=" O GLN f 287 " (cutoff:3.500A) removed outlier: 11.667A pdb=" N VAL f 286 " --> pdb=" O THR f 455 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N THR f 455 " --> pdb=" O VAL f 286 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N LEU f 288 " --> pdb=" O LEU f 453 " (cutoff:3.500A) removed outlier: 12.167A pdb=" N LEU f 453 " --> pdb=" O LEU f 288 " (cutoff:3.500A) removed outlier: 10.691A pdb=" N GLN f 290 " --> pdb=" O GLY f 451 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLY f 451 " --> pdb=" O GLN f 290 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR f 357 " --> pdb=" O GLU f 466 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE f 468 " --> pdb=" O THR f 357 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE f 359 " --> pdb=" O PHE f 468 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER f 393 " --> pdb=" O PHE f 361 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'f' and resid 302 through 312 removed outlier: 6.551A pdb=" N THR f 303 " --> pdb=" O GLY f 321 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE f 309 " --> pdb=" O GLN f 315 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLN f 315 " --> pdb=" O ILE f 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.524A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.524A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 58 through 59 removed outlier: 7.094A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR I 102 " --> pdb=" O LYS I 94 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 58 through 59 removed outlier: 7.094A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA I 88 " --> pdb=" O VAL I 109 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 100A through 100C Processing sheet with id=AC5, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.930A pdb=" N ILE M 54 " --> pdb=" O TRP M 41 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLN M 43 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N VAL M 52 " --> pdb=" O GLN M 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'h' and resid 494 through 499 removed outlier: 5.586A pdb=" N VAL i 608 " --> pdb=" O VAL h 36 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N VAL h 38 " --> pdb=" O THR i 606 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N THR i 606 " --> pdb=" O VAL h 38 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N TYR h 40 " --> pdb=" O CYS i 604 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N CYS i 604 " --> pdb=" O TYR h 40 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'h' and resid 45 through 47 Processing sheet with id=AC9, first strand: chain 'h' and resid 55 through 56 Processing sheet with id=AD1, first strand: chain 'h' and resid 66 through 67 removed outlier: 6.870A pdb=" N HIS h 66 " --> pdb=" O SER h 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'h' and resid 91 through 94 Processing sheet with id=AD3, first strand: chain 'h' and resid 202 through 203 removed outlier: 6.285A pdb=" N THR h 202 " --> pdb=" O TYR h 435 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'h' and resid 259 through 261 removed outlier: 3.801A pdb=" N GLY h 451 " --> pdb=" O LEU h 260 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE h 443 " --> pdb=" O ARG h 298 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY h 451 " --> pdb=" O GLN h 290 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N GLN h 290 " --> pdb=" O GLY h 451 " (cutoff:3.500A) removed outlier: 12.208A pdb=" N LEU h 453 " --> pdb=" O LEU h 288 " (cutoff:3.500A) removed outlier: 11.818A pdb=" N LEU h 288 " --> pdb=" O LEU h 453 " (cutoff:3.500A) removed outlier: 11.122A pdb=" N THR h 455 " --> pdb=" O VAL h 286 " (cutoff:3.500A) removed outlier: 11.713A pdb=" N VAL h 286 " --> pdb=" O THR h 455 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE h 297 " --> pdb=" O HIS h 330 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N HIS h 330 " --> pdb=" O ILE h 297 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'h' and resid 271 through 273 removed outlier: 3.560A pdb=" N THR h 271 " --> pdb=" O GLN h 287 " (cutoff:3.500A) removed outlier: 11.713A pdb=" N VAL h 286 " --> pdb=" O THR h 455 " (cutoff:3.500A) removed outlier: 11.122A pdb=" N THR h 455 " --> pdb=" O VAL h 286 " (cutoff:3.500A) removed outlier: 11.818A pdb=" N LEU h 288 " --> pdb=" O LEU h 453 " (cutoff:3.500A) removed outlier: 12.208A pdb=" N LEU h 453 " --> pdb=" O LEU h 288 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N GLN h 290 " --> pdb=" O GLY h 451 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY h 451 " --> pdb=" O GLN h 290 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE h 443 " --> pdb=" O ARG h 298 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR h 357 " --> pdb=" O GLU h 466 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N PHE h 468 " --> pdb=" O THR h 357 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE h 359 " --> pdb=" O PHE h 468 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER h 393 " --> pdb=" O PHE h 361 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'h' and resid 302 through 312 removed outlier: 6.540A pdb=" N THR h 303 " --> pdb=" O GLY h 321 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE h 309 " --> pdb=" O GLN h 315 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLN h 315 " --> pdb=" O ILE h 309 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.527A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.527A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 57 through 59 removed outlier: 7.122A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR J 102 " --> pdb=" O LYS J 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 57 through 59 removed outlier: 7.122A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA J 88 " --> pdb=" O VAL J 109 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AE3, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.925A pdb=" N ILE N 54 " --> pdb=" O TRP N 41 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLN N 43 " --> pdb=" O VAL N 52 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL N 52 " --> pdb=" O GLN N 43 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'j' and resid 494 through 499 removed outlier: 5.588A pdb=" N VAL k 608 " --> pdb=" O VAL j 36 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N VAL j 38 " --> pdb=" O THR k 606 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N THR k 606 " --> pdb=" O VAL j 38 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N TYR j 40 " --> pdb=" O CYS k 604 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N CYS k 604 " --> pdb=" O TYR j 40 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'j' and resid 45 through 47 Processing sheet with id=AE6, first strand: chain 'j' and resid 55 through 56 Processing sheet with id=AE7, first strand: chain 'j' and resid 91 through 94 Processing sheet with id=AE8, first strand: chain 'j' and resid 202 through 203 removed outlier: 6.292A pdb=" N THR j 202 " --> pdb=" O TYR j 435 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'j' and resid 259 through 261 removed outlier: 3.710A pdb=" N GLY j 451 " --> pdb=" O LEU j 260 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE j 443 " --> pdb=" O ARG j 298 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY j 451 " --> pdb=" O GLN j 290 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N GLN j 290 " --> pdb=" O GLY j 451 " (cutoff:3.500A) removed outlier: 12.194A pdb=" N LEU j 453 " --> pdb=" O LEU j 288 " (cutoff:3.500A) removed outlier: 11.912A pdb=" N LEU j 288 " --> pdb=" O LEU j 453 " (cutoff:3.500A) removed outlier: 11.081A pdb=" N THR j 455 " --> pdb=" O VAL j 286 " (cutoff:3.500A) removed outlier: 11.657A pdb=" N VAL j 286 " --> pdb=" O THR j 455 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE j 297 " --> pdb=" O HIS j 330 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS j 330 " --> pdb=" O ILE j 297 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE j 376 " --> pdb=" O PHE j 383 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'j' and resid 271 through 273 removed outlier: 3.579A pdb=" N THR j 271 " --> pdb=" O GLN j 287 " (cutoff:3.500A) removed outlier: 11.657A pdb=" N VAL j 286 " --> pdb=" O THR j 455 " (cutoff:3.500A) removed outlier: 11.081A pdb=" N THR j 455 " --> pdb=" O VAL j 286 " (cutoff:3.500A) removed outlier: 11.912A pdb=" N LEU j 288 " --> pdb=" O LEU j 453 " (cutoff:3.500A) removed outlier: 12.194A pdb=" N LEU j 453 " --> pdb=" O LEU j 288 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N GLN j 290 " --> pdb=" O GLY j 451 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY j 451 " --> pdb=" O GLN j 290 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE j 443 " --> pdb=" O ARG j 298 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR j 357 " --> pdb=" O GLU j 466 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N PHE j 468 " --> pdb=" O THR j 357 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE j 359 " --> pdb=" O PHE j 468 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER j 393 " --> pdb=" O PHE j 361 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'j' and resid 302 through 312 removed outlier: 6.533A pdb=" N THR j 303 " --> pdb=" O GLY j 321 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE j 309 " --> pdb=" O GLN j 315 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N GLN j 315 " --> pdb=" O ILE j 309 " (cutoff:3.500A) 742 hydrogen bonds defined for protein. 2010 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.97 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6271 1.34 - 1.46: 5407 1.46 - 1.58: 9514 1.58 - 1.70: 0 1.70 - 1.82: 162 Bond restraints: 21354 Sorted by residual: bond pdb=" C LYS f 117 " pdb=" N PRO f 118 " ideal model delta sigma weight residual 1.337 1.370 -0.034 1.06e-02 8.90e+03 1.02e+01 bond pdb=" C LYS j 117 " pdb=" N PRO j 118 " ideal model delta sigma weight residual 1.337 1.370 -0.034 1.06e-02 8.90e+03 1.00e+01 bond pdb=" C LYS h 117 " pdb=" N PRO h 118 " ideal model delta sigma weight residual 1.337 1.370 -0.033 1.06e-02 8.90e+03 9.84e+00 bond pdb=" N HIS f 66 " pdb=" CA HIS f 66 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.21e-02 6.83e+03 8.40e+00 bond pdb=" N HIS h 66 " pdb=" CA HIS h 66 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.16e+00 ... (remaining 21349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 28173 2.43 - 4.85: 684 4.85 - 7.28: 104 7.28 - 9.71: 27 9.71 - 12.14: 4 Bond angle restraints: 28992 Sorted by residual: angle pdb=" C ASN f 425 " pdb=" N MET f 426 " pdb=" CA MET f 426 " ideal model delta sigma weight residual 121.54 130.41 -8.87 1.91e+00 2.74e-01 2.16e+01 angle pdb=" C ASN h 425 " pdb=" N MET h 426 " pdb=" CA MET h 426 " ideal model delta sigma weight residual 121.54 130.21 -8.67 1.91e+00 2.74e-01 2.06e+01 angle pdb=" CA ASN j 339 " pdb=" CB ASN j 339 " pdb=" CG ASN j 339 " ideal model delta sigma weight residual 112.60 117.07 -4.47 1.00e+00 1.00e+00 2.00e+01 angle pdb=" CA ASN h 339 " pdb=" CB ASN h 339 " pdb=" CG ASN h 339 " ideal model delta sigma weight residual 112.60 117.07 -4.47 1.00e+00 1.00e+00 2.00e+01 angle pdb=" CA ASN f 339 " pdb=" CB ASN f 339 " pdb=" CG ASN f 339 " ideal model delta sigma weight residual 112.60 117.05 -4.45 1.00e+00 1.00e+00 1.98e+01 ... (remaining 28987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 13178 17.47 - 34.93: 895 34.93 - 52.40: 198 52.40 - 69.86: 106 69.86 - 87.33: 32 Dihedral angle restraints: 14409 sinusoidal: 7410 harmonic: 6999 Sorted by residual: dihedral pdb=" CB CYS f 54 " pdb=" SG CYS f 54 " pdb=" SG CYS f 74 " pdb=" CB CYS f 74 " ideal model delta sinusoidal sigma weight residual 93.00 5.67 87.33 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS h 54 " pdb=" SG CYS h 54 " pdb=" SG CYS h 74 " pdb=" CB CYS h 74 " ideal model delta sinusoidal sigma weight residual -86.00 -3.49 -82.51 1 1.00e+01 1.00e-02 8.35e+01 dihedral pdb=" CB CYS f 126 " pdb=" SG CYS f 126 " pdb=" SG CYS f 196 " pdb=" CB CYS f 196 " ideal model delta sinusoidal sigma weight residual 93.00 149.97 -56.97 1 1.00e+01 1.00e-02 4.37e+01 ... (remaining 14406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3100 0.080 - 0.161: 465 0.161 - 0.241: 23 0.241 - 0.322: 13 0.322 - 0.402: 2 Chirality restraints: 3603 Sorted by residual: chirality pdb=" C3 BMA q 3 " pdb=" C2 BMA q 3 " pdb=" C4 BMA q 3 " pdb=" O3 BMA q 3 " both_signs ideal model delta sigma weight residual False 2.41 2.01 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" C3 BMA X 3 " pdb=" C2 BMA X 3 " pdb=" C4 BMA X 3 " pdb=" O3 BMA X 3 " both_signs ideal model delta sigma weight residual False 2.41 2.03 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" C1 NAG j 601 " pdb=" ND2 ASN j 88 " pdb=" C2 NAG j 601 " pdb=" O5 NAG j 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 3600 not shown) Planarity restraints: 3567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL j 42 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO j 43 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO j 43 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO j 43 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL h 42 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO h 43 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO h 43 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO h 43 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL f 42 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO f 43 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO f 43 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO f 43 " -0.031 5.00e-02 4.00e+02 ... (remaining 3564 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5530 2.81 - 3.33: 18657 3.33 - 3.86: 34843 3.86 - 4.38: 37980 4.38 - 4.90: 67338 Nonbonded interactions: 164348 Sorted by model distance: nonbonded pdb=" O LEU i 661 " pdb=" OG1 THR j 499 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR f 499 " pdb=" O LEU k 661 " model vdw 2.289 3.040 nonbonded pdb=" O LEU g 661 " pdb=" OG1 THR h 499 " model vdw 2.290 3.040 nonbonded pdb=" O SER h 256 " pdb=" ND2 ASN h 478 " model vdw 2.310 3.120 nonbonded pdb=" OE1 GLU g 659 " pdb=" OH TYR h 39 " model vdw 2.334 3.040 ... (remaining 164343 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'l' selection = chain 'm' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'U' selection = chain 'W' selection = chain 'n' selection = chain 'p' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'V' selection = chain 'X' selection = chain 'o' selection = chain 'q' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'f' selection = chain 'h' selection = chain 'j' } ncs_group { reference = chain 'g' selection = chain 'i' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.04 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.230 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21528 Z= 0.194 Angle : 0.974 17.261 29472 Z= 0.497 Chirality : 0.056 0.402 3603 Planarity : 0.005 0.056 3498 Dihedral : 13.053 86.142 9789 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.16), residues: 2382 helix: -1.17 (0.22), residues: 405 sheet: -0.82 (0.19), residues: 705 loop : -1.35 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG k 542 TYR 0.034 0.002 TYR H 59 PHE 0.017 0.002 PHE J 100C TRP 0.027 0.002 TRP i 571 HIS 0.004 0.001 HIS j 249 Details of bonding type rmsd covalent geometry : bond 0.00375 (21354) covalent geometry : angle 0.93133 (28992) SS BOND : bond 0.00328 ( 42) SS BOND : angle 1.00555 ( 84) hydrogen bonds : bond 0.25254 ( 670) hydrogen bonds : angle 9.50235 ( 2010) link_ALPHA1-3 : bond 0.00614 ( 6) link_ALPHA1-3 : angle 3.72560 ( 18) link_ALPHA1-6 : bond 0.00323 ( 6) link_ALPHA1-6 : angle 1.58648 ( 18) link_BETA1-4 : bond 0.00741 ( 51) link_BETA1-4 : angle 1.89743 ( 153) link_NAG-ASN : bond 0.00431 ( 69) link_NAG-ASN : angle 3.02977 ( 207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8299 (mmt) cc_final: 0.8094 (mmm) REVERT: H 72 ASP cc_start: 0.8555 (m-30) cc_final: 0.8261 (t0) REVERT: H 75 LYS cc_start: 0.9454 (mptt) cc_final: 0.9138 (mtmm) REVERT: H 82 MET cc_start: 0.8744 (mmt) cc_final: 0.8159 (mmm) REVERT: H 96 ASP cc_start: 0.8565 (t0) cc_final: 0.8265 (t0) REVERT: H 99 ASP cc_start: 0.8501 (p0) cc_final: 0.8228 (p0) REVERT: H 100 LEU cc_start: 0.8783 (tt) cc_final: 0.8510 (pp) REVERT: H 100 TYR cc_start: 0.7749 (m-10) cc_final: 0.7446 (m-80) REVERT: L 97 GLU cc_start: 0.8992 (tp30) cc_final: 0.8574 (pm20) REVERT: L 105 HIS cc_start: 0.8755 (t-90) cc_final: 0.8064 (t70) REVERT: f 95 MET cc_start: 0.7933 (ptm) cc_final: 0.7511 (ptt) REVERT: f 104 MET cc_start: 0.9099 (ttt) cc_final: 0.8700 (ttt) REVERT: f 320 MET cc_start: 0.8202 (mpp) cc_final: 0.7954 (ptp) REVERT: f 434 MET cc_start: 0.7385 (tmm) cc_final: 0.7114 (tmm) REVERT: g 659 GLU cc_start: 0.8277 (tt0) cc_final: 0.8005 (tp30) REVERT: I 75 LYS cc_start: 0.9467 (mptt) cc_final: 0.9194 (mtmm) REVERT: I 82 MET cc_start: 0.8785 (mmt) cc_final: 0.8210 (mmm) REVERT: I 92 CYS cc_start: 0.1747 (t) cc_final: 0.1105 (t) REVERT: I 96 ASP cc_start: 0.8532 (t0) cc_final: 0.8289 (t0) REVERT: I 102 TYR cc_start: 0.8330 (m-80) cc_final: 0.8054 (m-80) REVERT: M 97 GLU cc_start: 0.9038 (tp30) cc_final: 0.8631 (pm20) REVERT: M 105 HIS cc_start: 0.8825 (t-90) cc_final: 0.8028 (t70) REVERT: h 95 MET cc_start: 0.7929 (ptm) cc_final: 0.7556 (ptt) REVERT: i 659 GLU cc_start: 0.8230 (tt0) cc_final: 0.7843 (tp30) REVERT: J 34 MET cc_start: 0.8370 (mmt) cc_final: 0.8096 (mmm) REVERT: J 52 ASN cc_start: 0.8491 (m110) cc_final: 0.8286 (m-40) REVERT: J 72 ASP cc_start: 0.8534 (m-30) cc_final: 0.8313 (t0) REVERT: J 75 LYS cc_start: 0.9512 (mptt) cc_final: 0.9196 (mtmm) REVERT: J 82 MET cc_start: 0.8583 (mmt) cc_final: 0.8008 (mmm) REVERT: J 100 TYR cc_start: 0.8027 (m-10) cc_final: 0.7330 (m-10) REVERT: J 102 TYR cc_start: 0.8283 (m-80) cc_final: 0.7920 (m-80) REVERT: N 97 GLU cc_start: 0.9061 (tp30) cc_final: 0.8653 (pm20) REVERT: N 105 HIS cc_start: 0.8805 (t-90) cc_final: 0.8041 (t70) REVERT: j 95 MET cc_start: 0.7871 (ptm) cc_final: 0.7452 (ptt) REVERT: j 104 MET cc_start: 0.9144 (ttt) cc_final: 0.8939 (ttt) REVERT: j 320 MET cc_start: 0.8272 (mpp) cc_final: 0.7964 (ptp) REVERT: k 647 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8451 (mt-10) REVERT: k 659 GLU cc_start: 0.8281 (tt0) cc_final: 0.7887 (tp30) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.1564 time to fit residues: 64.2918 Evaluate side-chains 182 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 30.0000 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN f 82 GLN f 185 ASN I 3 GLN h 82 GLN h 185 ASN h 422 GLN J 3 GLN j 185 ASN ** j 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 651 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.062584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.045837 restraints weight = 104953.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.047298 restraints weight = 56445.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.048083 restraints weight = 39485.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.048677 restraints weight = 32949.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.049028 restraints weight = 29090.066| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 21528 Z= 0.297 Angle : 0.824 14.783 29472 Z= 0.396 Chirality : 0.049 0.289 3603 Planarity : 0.005 0.047 3498 Dihedral : 7.711 58.333 5334 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.64 % Allowed : 11.16 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.16), residues: 2382 helix: -0.23 (0.25), residues: 417 sheet: -0.61 (0.20), residues: 627 loop : -1.11 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG g 644 TYR 0.034 0.002 TYR M 87 PHE 0.019 0.002 PHE f 391 TRP 0.019 0.002 TRP i 571 HIS 0.006 0.002 HIS f 374 Details of bonding type rmsd covalent geometry : bond 0.00654 (21354) covalent geometry : angle 0.77350 (28992) SS BOND : bond 0.00454 ( 42) SS BOND : angle 1.35594 ( 84) hydrogen bonds : bond 0.04874 ( 670) hydrogen bonds : angle 6.23737 ( 2010) link_ALPHA1-3 : bond 0.00672 ( 6) link_ALPHA1-3 : angle 2.62416 ( 18) link_ALPHA1-6 : bond 0.00126 ( 6) link_ALPHA1-6 : angle 1.70087 ( 18) link_BETA1-4 : bond 0.00512 ( 51) link_BETA1-4 : angle 2.05767 ( 153) link_NAG-ASN : bond 0.00534 ( 69) link_NAG-ASN : angle 2.85147 ( 207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 165 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 PHE cc_start: 0.7943 (p90) cc_final: 0.7663 (p90) REVERT: H 100 TYR cc_start: 0.8275 (m-10) cc_final: 0.7626 (m-10) REVERT: L 42 TYR cc_start: 0.6940 (m-80) cc_final: 0.6614 (m-10) REVERT: L 66 ASN cc_start: 0.7908 (m-40) cc_final: 0.7550 (m-40) REVERT: L 97 GLU cc_start: 0.9047 (tp30) cc_final: 0.8661 (pm20) REVERT: f 95 MET cc_start: 0.8230 (ptm) cc_final: 0.7622 (ptt) REVERT: f 434 MET cc_start: 0.7977 (tmm) cc_final: 0.7232 (tmm) REVERT: g 520 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7949 (mpp80) REVERT: g 633 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8521 (mttm) REVERT: g 659 GLU cc_start: 0.8706 (tt0) cc_final: 0.8177 (tp30) REVERT: I 100 ASP cc_start: 0.7560 (m-30) cc_final: 0.7160 (m-30) REVERT: M 42 TYR cc_start: 0.6858 (m-80) cc_final: 0.6542 (m-10) REVERT: M 66 ASN cc_start: 0.7994 (m-40) cc_final: 0.7711 (m-40) REVERT: M 87 TYR cc_start: 0.7829 (m-80) cc_final: 0.7082 (m-10) REVERT: M 97 GLU cc_start: 0.9088 (tp30) cc_final: 0.8711 (pm20) REVERT: h 95 MET cc_start: 0.8339 (ptm) cc_final: 0.7807 (ptt) REVERT: h 104 MET cc_start: 0.9265 (ttt) cc_final: 0.9048 (ttm) REVERT: h 320 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8051 (ptp) REVERT: i 530 MET cc_start: 0.8563 (mtm) cc_final: 0.7569 (mtm) REVERT: i 633 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8511 (mttm) REVERT: i 648 GLU cc_start: 0.8969 (pp20) cc_final: 0.8763 (pp20) REVERT: i 659 GLU cc_start: 0.8596 (tt0) cc_final: 0.8202 (tp30) REVERT: J 72 ASP cc_start: 0.8697 (m-30) cc_final: 0.8133 (t0) REVERT: J 75 LYS cc_start: 0.9613 (mptt) cc_final: 0.9192 (mtmm) REVERT: J 96 ASP cc_start: 0.8662 (t0) cc_final: 0.8457 (t0) REVERT: J 100 ASP cc_start: 0.7967 (m-30) cc_final: 0.7563 (m-30) REVERT: N 42 TYR cc_start: 0.6881 (m-80) cc_final: 0.6536 (m-10) REVERT: N 66 ASN cc_start: 0.7969 (m-40) cc_final: 0.7586 (m-40) REVERT: N 87 TYR cc_start: 0.7827 (m-80) cc_final: 0.7058 (m-10) REVERT: N 97 GLU cc_start: 0.9031 (tp30) cc_final: 0.8657 (pm20) REVERT: j 95 MET cc_start: 0.8263 (ptm) cc_final: 0.7739 (ptt) REVERT: k 633 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8516 (mttm) REVERT: k 659 GLU cc_start: 0.8561 (tt0) cc_final: 0.8116 (tp30) outliers start: 56 outliers final: 34 residues processed: 212 average time/residue: 0.1589 time to fit residues: 51.8006 Evaluate side-chains 181 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 86 LEU Chi-restraints excluded: chain f residue 297 ILE Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain f residue 494 LEU Chi-restraints excluded: chain f residue 496 VAL Chi-restraints excluded: chain g residue 520 ARG Chi-restraints excluded: chain g residue 545 LEU Chi-restraints excluded: chain g residue 546 SER Chi-restraints excluded: chain g residue 583 VAL Chi-restraints excluded: chain g residue 633 LYS Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 320 MET Chi-restraints excluded: chain h residue 488 VAL Chi-restraints excluded: chain h residue 496 VAL Chi-restraints excluded: chain i residue 545 LEU Chi-restraints excluded: chain i residue 546 SER Chi-restraints excluded: chain i residue 583 VAL Chi-restraints excluded: chain i residue 630 GLN Chi-restraints excluded: chain i residue 633 LYS Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain j residue 86 LEU Chi-restraints excluded: chain j residue 126 CYS Chi-restraints excluded: chain j residue 297 ILE Chi-restraints excluded: chain j residue 477 ASP Chi-restraints excluded: chain j residue 488 VAL Chi-restraints excluded: chain j residue 494 LEU Chi-restraints excluded: chain j residue 496 VAL Chi-restraints excluded: chain k residue 545 LEU Chi-restraints excluded: chain k residue 546 SER Chi-restraints excluded: chain k residue 583 VAL Chi-restraints excluded: chain k residue 630 GLN Chi-restraints excluded: chain k residue 633 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 234 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 174 optimal weight: 20.0000 chunk 151 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 563 GLN j 195 ASN j 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.063637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.046931 restraints weight = 103285.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.048460 restraints weight = 54724.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.049278 restraints weight = 37835.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.049923 restraints weight = 31345.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.050239 restraints weight = 27318.412| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21528 Z= 0.138 Angle : 0.665 14.299 29472 Z= 0.313 Chirality : 0.047 0.284 3603 Planarity : 0.004 0.045 3498 Dihedral : 7.485 58.502 5334 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.35 % Allowed : 12.99 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.17), residues: 2382 helix: 0.27 (0.26), residues: 399 sheet: -0.49 (0.20), residues: 627 loop : -0.82 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG i 519 TYR 0.018 0.001 TYR M 87 PHE 0.009 0.001 PHE I 100C TRP 0.039 0.002 TRP M 107 HIS 0.004 0.001 HIS N 105 Details of bonding type rmsd covalent geometry : bond 0.00310 (21354) covalent geometry : angle 0.61412 (28992) SS BOND : bond 0.00324 ( 42) SS BOND : angle 0.77334 ( 84) hydrogen bonds : bond 0.04016 ( 670) hydrogen bonds : angle 5.64028 ( 2010) link_ALPHA1-3 : bond 0.00548 ( 6) link_ALPHA1-3 : angle 3.01661 ( 18) link_ALPHA1-6 : bond 0.00245 ( 6) link_ALPHA1-6 : angle 1.62841 ( 18) link_BETA1-4 : bond 0.00471 ( 51) link_BETA1-4 : angle 1.71914 ( 153) link_NAG-ASN : bond 0.00348 ( 69) link_NAG-ASN : angle 2.59165 ( 207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 163 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.7991 (mmt) cc_final: 0.7695 (mmm) REVERT: H 48 ILE cc_start: 0.9639 (OUTLIER) cc_final: 0.9179 (mm) REVERT: H 79 PHE cc_start: 0.8207 (p90) cc_final: 0.7441 (p90) REVERT: H 82 LEU cc_start: 0.9324 (pt) cc_final: 0.8953 (tt) REVERT: H 96 ASP cc_start: 0.8546 (t0) cc_final: 0.8207 (t0) REVERT: H 100 ASP cc_start: 0.7584 (m-30) cc_final: 0.6691 (m-30) REVERT: H 100 LEU cc_start: 0.8316 (mp) cc_final: 0.8107 (pp) REVERT: L 42 TYR cc_start: 0.6984 (m-80) cc_final: 0.6590 (m-80) REVERT: L 66 ASN cc_start: 0.7912 (m-40) cc_final: 0.7500 (m-40) REVERT: L 97 GLU cc_start: 0.9041 (tp30) cc_final: 0.8666 (pm20) REVERT: L 105 HIS cc_start: 0.8662 (t-90) cc_final: 0.7905 (t70) REVERT: f 95 MET cc_start: 0.8168 (ptm) cc_final: 0.7595 (ptt) REVERT: f 320 MET cc_start: 0.8234 (ptp) cc_final: 0.7961 (ptp) REVERT: f 434 MET cc_start: 0.7818 (tmm) cc_final: 0.7335 (tmm) REVERT: g 530 MET cc_start: 0.8345 (mtm) cc_final: 0.7518 (mtm) REVERT: g 633 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8397 (mttm) REVERT: g 644 ARG cc_start: 0.9241 (mmp80) cc_final: 0.8917 (mmp80) REVERT: g 647 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8744 (mp0) REVERT: g 659 GLU cc_start: 0.8669 (tt0) cc_final: 0.8285 (tp30) REVERT: I 78 LEU cc_start: 0.9283 (tp) cc_final: 0.8787 (tt) REVERT: I 82 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9192 (pt) REVERT: I 100 ASP cc_start: 0.7463 (m-30) cc_final: 0.7034 (m-30) REVERT: M 42 TYR cc_start: 0.6806 (m-80) cc_final: 0.6426 (m-80) REVERT: M 66 ASN cc_start: 0.7924 (m-40) cc_final: 0.7561 (m-40) REVERT: M 97 GLU cc_start: 0.9048 (tp30) cc_final: 0.8710 (pm20) REVERT: M 105 HIS cc_start: 0.8603 (t-90) cc_final: 0.7861 (t70) REVERT: h 95 MET cc_start: 0.8239 (ptm) cc_final: 0.7778 (ptt) REVERT: h 104 MET cc_start: 0.9258 (ttt) cc_final: 0.9038 (ttm) REVERT: i 530 MET cc_start: 0.8502 (mtm) cc_final: 0.7484 (mtm) REVERT: i 633 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8344 (mttm) REVERT: i 659 GLU cc_start: 0.8521 (tt0) cc_final: 0.8179 (tp30) REVERT: J 34 MET cc_start: 0.7942 (mmt) cc_final: 0.7669 (mmm) REVERT: J 45 LEU cc_start: 0.8349 (tp) cc_final: 0.8049 (mm) REVERT: J 72 ASP cc_start: 0.8701 (m-30) cc_final: 0.8151 (t0) REVERT: J 75 LYS cc_start: 0.9612 (mptt) cc_final: 0.9179 (mtmm) REVERT: J 82 MET cc_start: 0.9128 (mmm) cc_final: 0.8702 (mmm) REVERT: J 82 LEU cc_start: 0.9096 (tt) cc_final: 0.8568 (mp) REVERT: J 96 ASP cc_start: 0.8664 (t0) cc_final: 0.8449 (t0) REVERT: J 100 ASP cc_start: 0.7952 (m-30) cc_final: 0.7518 (m-30) REVERT: J 100 TYR cc_start: 0.8107 (m-10) cc_final: 0.7717 (m-10) REVERT: N 11 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6396 (mpp) REVERT: N 42 TYR cc_start: 0.6945 (m-80) cc_final: 0.6367 (m-80) REVERT: N 97 GLU cc_start: 0.9080 (tp30) cc_final: 0.8708 (pm20) REVERT: j 95 MET cc_start: 0.8202 (ptm) cc_final: 0.7662 (ptt) REVERT: j 100 MET cc_start: 0.8937 (mtm) cc_final: 0.8691 (mtm) REVERT: j 104 MET cc_start: 0.9328 (ttm) cc_final: 0.9091 (ttm) REVERT: j 320 MET cc_start: 0.8179 (ptp) cc_final: 0.7958 (ptp) REVERT: k 633 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8425 (mttm) REVERT: k 644 ARG cc_start: 0.9175 (mmp80) cc_final: 0.8744 (mmp80) REVERT: k 647 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8649 (mt-10) REVERT: k 659 GLU cc_start: 0.8535 (tt0) cc_final: 0.8239 (tp30) outliers start: 50 outliers final: 27 residues processed: 200 average time/residue: 0.1611 time to fit residues: 49.3900 Evaluate side-chains 175 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain f residue 86 LEU Chi-restraints excluded: chain f residue 181 ILE Chi-restraints excluded: chain f residue 496 VAL Chi-restraints excluded: chain g residue 546 SER Chi-restraints excluded: chain g residue 583 VAL Chi-restraints excluded: chain g residue 603 ILE Chi-restraints excluded: chain g residue 633 LYS Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain h residue 181 ILE Chi-restraints excluded: chain h residue 496 VAL Chi-restraints excluded: chain i residue 545 LEU Chi-restraints excluded: chain i residue 546 SER Chi-restraints excluded: chain i residue 583 VAL Chi-restraints excluded: chain i residue 603 ILE Chi-restraints excluded: chain i residue 633 LYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain N residue 11 MET Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 101 VAL Chi-restraints excluded: chain j residue 297 ILE Chi-restraints excluded: chain j residue 496 VAL Chi-restraints excluded: chain k residue 545 LEU Chi-restraints excluded: chain k residue 546 SER Chi-restraints excluded: chain k residue 583 VAL Chi-restraints excluded: chain k residue 603 ILE Chi-restraints excluded: chain k residue 633 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 189 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 563 GLN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.063054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.046324 restraints weight = 103837.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.047835 restraints weight = 55050.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.048776 restraints weight = 38138.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.049266 restraints weight = 30792.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.049632 restraints weight = 27598.212| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21528 Z= 0.166 Angle : 0.660 14.269 29472 Z= 0.311 Chirality : 0.046 0.275 3603 Planarity : 0.003 0.046 3498 Dihedral : 7.478 57.323 5334 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.97 % Allowed : 12.85 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.17), residues: 2382 helix: 0.28 (0.26), residues: 417 sheet: -0.54 (0.20), residues: 663 loop : -0.81 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG i 644 TYR 0.030 0.001 TYR N 87 PHE 0.012 0.001 PHE H 79 TRP 0.042 0.001 TRP M 107 HIS 0.003 0.001 HIS N 105 Details of bonding type rmsd covalent geometry : bond 0.00371 (21354) covalent geometry : angle 0.60983 (28992) SS BOND : bond 0.00266 ( 42) SS BOND : angle 0.67469 ( 84) hydrogen bonds : bond 0.03727 ( 670) hydrogen bonds : angle 5.40241 ( 2010) link_ALPHA1-3 : bond 0.00556 ( 6) link_ALPHA1-3 : angle 2.81565 ( 18) link_ALPHA1-6 : bond 0.00202 ( 6) link_ALPHA1-6 : angle 1.62326 ( 18) link_BETA1-4 : bond 0.00445 ( 51) link_BETA1-4 : angle 1.71381 ( 153) link_NAG-ASN : bond 0.00372 ( 69) link_NAG-ASN : angle 2.59244 ( 207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 147 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8087 (mmt) cc_final: 0.7690 (tpt) REVERT: H 79 PHE cc_start: 0.8231 (p90) cc_final: 0.7485 (p90) REVERT: H 82 LEU cc_start: 0.9345 (pt) cc_final: 0.9015 (tt) REVERT: H 96 ASP cc_start: 0.8580 (t0) cc_final: 0.8231 (t0) REVERT: H 100 ASP cc_start: 0.7620 (m-30) cc_final: 0.6457 (m-30) REVERT: H 100 LEU cc_start: 0.8187 (mp) cc_final: 0.7893 (pp) REVERT: L 4 LEU cc_start: 0.8342 (mm) cc_final: 0.7730 (tp) REVERT: L 42 TYR cc_start: 0.7043 (m-80) cc_final: 0.6130 (m-10) REVERT: L 66 ASN cc_start: 0.7929 (m-40) cc_final: 0.7486 (m-40) REVERT: L 87 TYR cc_start: 0.7933 (m-80) cc_final: 0.7069 (m-10) REVERT: L 97 GLU cc_start: 0.9111 (tp30) cc_final: 0.8745 (pm20) REVERT: f 95 MET cc_start: 0.8201 (ptm) cc_final: 0.7725 (ptm) REVERT: f 320 MET cc_start: 0.8310 (ptp) cc_final: 0.7571 (ptp) REVERT: f 434 MET cc_start: 0.7900 (tmm) cc_final: 0.7458 (tmm) REVERT: g 530 MET cc_start: 0.8521 (mtm) cc_final: 0.7721 (mtm) REVERT: g 633 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8393 (mttm) REVERT: g 659 GLU cc_start: 0.8674 (tt0) cc_final: 0.8273 (tp30) REVERT: I 34 MET cc_start: 0.8030 (mmt) cc_final: 0.7696 (tpt) REVERT: I 75 LYS cc_start: 0.9454 (pttp) cc_final: 0.9152 (pttm) REVERT: I 78 LEU cc_start: 0.9251 (tp) cc_final: 0.8925 (tt) REVERT: I 82 LEU cc_start: 0.9403 (mp) cc_final: 0.9168 (pt) REVERT: I 100 ASP cc_start: 0.7435 (m-30) cc_final: 0.7116 (m-30) REVERT: M 4 LEU cc_start: 0.8357 (mm) cc_final: 0.7998 (tp) REVERT: M 11 MET cc_start: 0.6655 (OUTLIER) cc_final: 0.6426 (mpp) REVERT: M 42 TYR cc_start: 0.6951 (m-80) cc_final: 0.6096 (m-10) REVERT: M 66 ASN cc_start: 0.7902 (m-40) cc_final: 0.7577 (m-40) REVERT: M 87 TYR cc_start: 0.7851 (m-80) cc_final: 0.7039 (m-10) REVERT: M 97 GLU cc_start: 0.9111 (tp30) cc_final: 0.8774 (pm20) REVERT: h 95 MET cc_start: 0.8295 (ptm) cc_final: 0.7835 (ptt) REVERT: h 104 MET cc_start: 0.9286 (ttt) cc_final: 0.9041 (ttm) REVERT: h 320 MET cc_start: 0.8388 (ptp) cc_final: 0.7945 (ptp) REVERT: i 530 MET cc_start: 0.8518 (mtm) cc_final: 0.7586 (mtm) REVERT: i 633 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8375 (mttm) REVERT: i 659 GLU cc_start: 0.8532 (tt0) cc_final: 0.7991 (tp30) REVERT: J 45 LEU cc_start: 0.8464 (tp) cc_final: 0.8113 (mm) REVERT: J 72 ASP cc_start: 0.8710 (m-30) cc_final: 0.8157 (t0) REVERT: J 75 LYS cc_start: 0.9631 (mptt) cc_final: 0.9172 (mtmm) REVERT: J 78 LEU cc_start: 0.9260 (tp) cc_final: 0.8883 (tt) REVERT: J 82 LEU cc_start: 0.9092 (tt) cc_final: 0.8790 (tt) REVERT: J 96 ASP cc_start: 0.8702 (t0) cc_final: 0.8478 (t0) REVERT: J 100 ASP cc_start: 0.8272 (m-30) cc_final: 0.7706 (m-30) REVERT: J 100 TYR cc_start: 0.8045 (m-10) cc_final: 0.7734 (m-10) REVERT: N 4 LEU cc_start: 0.8318 (mm) cc_final: 0.7670 (tp) REVERT: N 42 TYR cc_start: 0.7025 (m-80) cc_final: 0.6104 (m-10) REVERT: N 66 ASN cc_start: 0.7815 (m-40) cc_final: 0.7448 (m110) REVERT: N 87 TYR cc_start: 0.7799 (m-80) cc_final: 0.7033 (m-10) REVERT: N 97 GLU cc_start: 0.9146 (tp30) cc_final: 0.8760 (pm20) REVERT: j 95 MET cc_start: 0.8248 (ptm) cc_final: 0.7729 (ptt) REVERT: j 104 MET cc_start: 0.9345 (ttm) cc_final: 0.9001 (ttm) REVERT: j 320 MET cc_start: 0.8162 (ptp) cc_final: 0.7932 (ptp) REVERT: k 633 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8451 (mttm) REVERT: k 659 GLU cc_start: 0.8530 (tt0) cc_final: 0.8225 (tp30) outliers start: 63 outliers final: 42 residues processed: 201 average time/residue: 0.1587 time to fit residues: 49.5446 Evaluate side-chains 183 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 137 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain f residue 86 LEU Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 181 ILE Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain f residue 496 VAL Chi-restraints excluded: chain g residue 545 LEU Chi-restraints excluded: chain g residue 546 SER Chi-restraints excluded: chain g residue 583 VAL Chi-restraints excluded: chain g residue 603 ILE Chi-restraints excluded: chain g residue 630 GLN Chi-restraints excluded: chain g residue 633 LYS Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain M residue 11 MET Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain h residue 123 THR Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 181 ILE Chi-restraints excluded: chain h residue 496 VAL Chi-restraints excluded: chain i residue 545 LEU Chi-restraints excluded: chain i residue 546 SER Chi-restraints excluded: chain i residue 583 VAL Chi-restraints excluded: chain i residue 603 ILE Chi-restraints excluded: chain i residue 633 LYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 101 VAL Chi-restraints excluded: chain j residue 123 THR Chi-restraints excluded: chain j residue 126 CYS Chi-restraints excluded: chain j residue 127 VAL Chi-restraints excluded: chain j residue 297 ILE Chi-restraints excluded: chain j residue 488 VAL Chi-restraints excluded: chain j residue 496 VAL Chi-restraints excluded: chain k residue 545 LEU Chi-restraints excluded: chain k residue 546 SER Chi-restraints excluded: chain k residue 583 VAL Chi-restraints excluded: chain k residue 603 ILE Chi-restraints excluded: chain k residue 633 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 160 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 99 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 chunk 227 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 232 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 99 ASN f 422 GLN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 114 GLN k 563 GLN ** k 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.061079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.044514 restraints weight = 105226.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.045947 restraints weight = 56209.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.046704 restraints weight = 39207.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.047301 restraints weight = 32714.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.047620 restraints weight = 28552.454| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 21528 Z= 0.307 Angle : 0.781 13.864 29472 Z= 0.373 Chirality : 0.048 0.262 3603 Planarity : 0.004 0.047 3498 Dihedral : 7.893 58.404 5334 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.33 % Allowed : 12.10 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.17), residues: 2382 helix: -0.00 (0.26), residues: 399 sheet: -0.50 (0.20), residues: 663 loop : -0.82 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 83 TYR 0.031 0.002 TYR N 87 PHE 0.016 0.002 PHE f 391 TRP 0.051 0.002 TRP N 107 HIS 0.005 0.001 HIS h 72 Details of bonding type rmsd covalent geometry : bond 0.00682 (21354) covalent geometry : angle 0.73397 (28992) SS BOND : bond 0.00369 ( 42) SS BOND : angle 0.96849 ( 84) hydrogen bonds : bond 0.04264 ( 670) hydrogen bonds : angle 5.55802 ( 2010) link_ALPHA1-3 : bond 0.00633 ( 6) link_ALPHA1-3 : angle 2.64586 ( 18) link_ALPHA1-6 : bond 0.00143 ( 6) link_ALPHA1-6 : angle 1.66411 ( 18) link_BETA1-4 : bond 0.00473 ( 51) link_BETA1-4 : angle 1.90413 ( 153) link_NAG-ASN : bond 0.00603 ( 69) link_NAG-ASN : angle 2.75216 ( 207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 128 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8085 (mmt) cc_final: 0.7814 (mmm) REVERT: H 82 LEU cc_start: 0.9339 (pt) cc_final: 0.9023 (tt) REVERT: H 96 ASP cc_start: 0.8634 (t0) cc_final: 0.8370 (t0) REVERT: H 100 ASP cc_start: 0.8104 (m-30) cc_final: 0.7692 (m-30) REVERT: L 4 LEU cc_start: 0.8528 (mm) cc_final: 0.8178 (tp) REVERT: L 11 MET cc_start: 0.6577 (mtm) cc_final: 0.6371 (mpp) REVERT: L 42 TYR cc_start: 0.7324 (m-80) cc_final: 0.6563 (m-10) REVERT: L 66 ASN cc_start: 0.7832 (m-40) cc_final: 0.7410 (m-40) REVERT: L 87 TYR cc_start: 0.7912 (m-80) cc_final: 0.7002 (m-10) REVERT: L 97 GLU cc_start: 0.9125 (tp30) cc_final: 0.8751 (pm20) REVERT: f 95 MET cc_start: 0.8256 (ptm) cc_final: 0.7730 (ptt) REVERT: f 320 MET cc_start: 0.8352 (ptp) cc_final: 0.8129 (ptp) REVERT: f 434 MET cc_start: 0.7973 (tmm) cc_final: 0.7384 (tmm) REVERT: g 530 MET cc_start: 0.8591 (mtm) cc_final: 0.7615 (mtm) REVERT: g 633 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8482 (mttm) REVERT: g 659 GLU cc_start: 0.8681 (tt0) cc_final: 0.8168 (tp30) REVERT: I 34 MET cc_start: 0.8181 (mmt) cc_final: 0.7896 (tpt) REVERT: I 78 LEU cc_start: 0.9305 (tp) cc_final: 0.8959 (tt) REVERT: M 4 LEU cc_start: 0.8534 (mm) cc_final: 0.8139 (tp) REVERT: M 11 MET cc_start: 0.6638 (OUTLIER) cc_final: 0.6397 (mpp) REVERT: M 42 TYR cc_start: 0.7223 (m-80) cc_final: 0.6456 (m-10) REVERT: M 66 ASN cc_start: 0.7860 (m-40) cc_final: 0.7557 (m-40) REVERT: M 87 TYR cc_start: 0.7836 (m-80) cc_final: 0.7031 (m-10) REVERT: M 97 GLU cc_start: 0.9043 (tp30) cc_final: 0.8709 (pm20) REVERT: h 95 MET cc_start: 0.8328 (ptm) cc_final: 0.7877 (ptm) REVERT: h 104 MET cc_start: 0.9364 (ttt) cc_final: 0.9140 (ttm) REVERT: h 320 MET cc_start: 0.8512 (ptp) cc_final: 0.8287 (ptp) REVERT: i 520 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8206 (mpp80) REVERT: i 530 MET cc_start: 0.8604 (mtm) cc_final: 0.7616 (mtm) REVERT: i 633 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8527 (mttm) REVERT: i 659 GLU cc_start: 0.8679 (tt0) cc_final: 0.8066 (tp30) REVERT: J 45 LEU cc_start: 0.8563 (tp) cc_final: 0.8194 (mm) REVERT: J 72 ASP cc_start: 0.8680 (m-30) cc_final: 0.8063 (t0) REVERT: J 75 LYS cc_start: 0.9659 (mptt) cc_final: 0.9210 (mtmm) REVERT: J 78 LEU cc_start: 0.9289 (tp) cc_final: 0.8944 (tt) REVERT: J 82 MET cc_start: 0.9239 (mmm) cc_final: 0.9019 (mmm) REVERT: J 82 LEU cc_start: 0.9062 (tt) cc_final: 0.8819 (tt) REVERT: J 96 ASP cc_start: 0.8717 (t0) cc_final: 0.8497 (t0) REVERT: J 100 ASP cc_start: 0.8365 (m-30) cc_final: 0.7809 (m-30) REVERT: N 11 MET cc_start: 0.6829 (mtp) cc_final: 0.6378 (mpp) REVERT: N 66 ASN cc_start: 0.7728 (m-40) cc_final: 0.7370 (m110) REVERT: N 87 TYR cc_start: 0.7823 (m-80) cc_final: 0.6955 (m-10) REVERT: N 97 GLU cc_start: 0.9163 (tp30) cc_final: 0.8787 (pm20) REVERT: j 95 MET cc_start: 0.8267 (ptm) cc_final: 0.7749 (ptt) REVERT: j 320 MET cc_start: 0.8293 (ptp) cc_final: 0.7870 (ptp) REVERT: k 530 MET cc_start: 0.8626 (mtm) cc_final: 0.7638 (mtm) REVERT: k 633 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8531 (mttm) REVERT: k 659 GLU cc_start: 0.8601 (tt0) cc_final: 0.8152 (tp30) outliers start: 92 outliers final: 61 residues processed: 213 average time/residue: 0.1518 time to fit residues: 51.0939 Evaluate side-chains 187 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 121 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 181 ILE Chi-restraints excluded: chain f residue 187 ASN Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain f residue 494 LEU Chi-restraints excluded: chain f residue 496 VAL Chi-restraints excluded: chain g residue 545 LEU Chi-restraints excluded: chain g residue 546 SER Chi-restraints excluded: chain g residue 583 VAL Chi-restraints excluded: chain g residue 603 ILE Chi-restraints excluded: chain g residue 633 LYS Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain M residue 11 MET Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain h residue 120 VAL Chi-restraints excluded: chain h residue 123 THR Chi-restraints excluded: chain h residue 125 LEU Chi-restraints excluded: chain h residue 126 CYS Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 181 ILE Chi-restraints excluded: chain h residue 187 ASN Chi-restraints excluded: chain h residue 488 VAL Chi-restraints excluded: chain h residue 496 VAL Chi-restraints excluded: chain i residue 520 ARG Chi-restraints excluded: chain i residue 545 LEU Chi-restraints excluded: chain i residue 546 SER Chi-restraints excluded: chain i residue 583 VAL Chi-restraints excluded: chain i residue 603 ILE Chi-restraints excluded: chain i residue 633 LYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 86 LEU Chi-restraints excluded: chain j residue 101 VAL Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 123 THR Chi-restraints excluded: chain j residue 125 LEU Chi-restraints excluded: chain j residue 126 CYS Chi-restraints excluded: chain j residue 127 VAL Chi-restraints excluded: chain j residue 187 ASN Chi-restraints excluded: chain j residue 297 ILE Chi-restraints excluded: chain j residue 477 ASP Chi-restraints excluded: chain j residue 488 VAL Chi-restraints excluded: chain j residue 494 LEU Chi-restraints excluded: chain j residue 496 VAL Chi-restraints excluded: chain k residue 545 LEU Chi-restraints excluded: chain k residue 546 SER Chi-restraints excluded: chain k residue 583 VAL Chi-restraints excluded: chain k residue 603 ILE Chi-restraints excluded: chain k residue 633 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 149 optimal weight: 6.9990 chunk 212 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 205 optimal weight: 0.9980 chunk 156 optimal weight: 0.6980 chunk 211 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 99 ASN h 114 GLN i 616 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.062735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.046167 restraints weight = 102785.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.047600 restraints weight = 54351.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.048526 restraints weight = 37733.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.049060 restraints weight = 30439.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.049085 restraints weight = 26979.676| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21528 Z= 0.127 Angle : 0.647 13.813 29472 Z= 0.305 Chirality : 0.046 0.268 3603 Planarity : 0.003 0.050 3498 Dihedral : 7.599 59.797 5334 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.97 % Allowed : 13.89 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.17), residues: 2382 helix: -0.09 (0.26), residues: 435 sheet: -0.55 (0.19), residues: 678 loop : -0.70 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG i 644 TYR 0.019 0.001 TYR N 87 PHE 0.012 0.001 PHE H 100C TRP 0.066 0.002 TRP N 107 HIS 0.003 0.001 HIS f 374 Details of bonding type rmsd covalent geometry : bond 0.00292 (21354) covalent geometry : angle 0.59917 (28992) SS BOND : bond 0.00319 ( 42) SS BOND : angle 0.65629 ( 84) hydrogen bonds : bond 0.03533 ( 670) hydrogen bonds : angle 5.20036 ( 2010) link_ALPHA1-3 : bond 0.00439 ( 6) link_ALPHA1-3 : angle 2.87330 ( 18) link_ALPHA1-6 : bond 0.00334 ( 6) link_ALPHA1-6 : angle 1.55506 ( 18) link_BETA1-4 : bond 0.00427 ( 51) link_BETA1-4 : angle 1.59815 ( 153) link_NAG-ASN : bond 0.00322 ( 69) link_NAG-ASN : angle 2.51612 ( 207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 133 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 ASN cc_start: 0.8103 (t0) cc_final: 0.7585 (t0) REVERT: H 82 LEU cc_start: 0.9277 (pt) cc_final: 0.8939 (tt) REVERT: H 100 ASP cc_start: 0.7883 (m-30) cc_final: 0.6981 (m-30) REVERT: H 100 LEU cc_start: 0.8256 (mp) cc_final: 0.7774 (pp) REVERT: L 4 LEU cc_start: 0.8426 (mm) cc_final: 0.8147 (tp) REVERT: L 11 MET cc_start: 0.6493 (OUTLIER) cc_final: 0.6268 (mpp) REVERT: L 42 TYR cc_start: 0.7165 (m-80) cc_final: 0.6904 (m-10) REVERT: L 66 ASN cc_start: 0.7795 (m-40) cc_final: 0.7338 (m-40) REVERT: L 97 GLU cc_start: 0.9121 (tp30) cc_final: 0.8766 (pm20) REVERT: f 83 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: f 95 MET cc_start: 0.8213 (ptm) cc_final: 0.7708 (ptt) REVERT: f 320 MET cc_start: 0.8269 (ptp) cc_final: 0.7869 (ptp) REVERT: f 434 MET cc_start: 0.7786 (tmm) cc_final: 0.7567 (tmm) REVERT: g 530 MET cc_start: 0.8504 (mtm) cc_final: 0.7728 (mtm) REVERT: g 633 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8445 (mttm) REVERT: g 659 GLU cc_start: 0.8651 (tt0) cc_final: 0.8154 (tp30) REVERT: I 34 MET cc_start: 0.8267 (mmt) cc_final: 0.7929 (tpt) REVERT: I 78 LEU cc_start: 0.9271 (tp) cc_final: 0.8926 (tt) REVERT: M 4 LEU cc_start: 0.8425 (mm) cc_final: 0.8114 (tp) REVERT: M 66 ASN cc_start: 0.7851 (m-40) cc_final: 0.7553 (m-40) REVERT: M 97 GLU cc_start: 0.9093 (tp30) cc_final: 0.8759 (pm20) REVERT: h 95 MET cc_start: 0.8297 (ptm) cc_final: 0.7916 (ptt) REVERT: h 104 MET cc_start: 0.9315 (ttt) cc_final: 0.9053 (ttm) REVERT: h 320 MET cc_start: 0.8377 (ptp) cc_final: 0.7956 (ptp) REVERT: h 434 MET cc_start: 0.7751 (tmm) cc_final: 0.7464 (tmm) REVERT: i 530 MET cc_start: 0.8435 (mtm) cc_final: 0.7526 (mtm) REVERT: i 633 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8524 (mttm) REVERT: i 659 GLU cc_start: 0.8699 (tt0) cc_final: 0.8073 (tp30) REVERT: J 45 LEU cc_start: 0.8634 (tp) cc_final: 0.8317 (mm) REVERT: J 72 ASP cc_start: 0.8657 (m-30) cc_final: 0.8095 (t0) REVERT: J 75 LYS cc_start: 0.9645 (mptt) cc_final: 0.9175 (mtmm) REVERT: J 78 LEU cc_start: 0.9250 (tp) cc_final: 0.8875 (tt) REVERT: J 82 LEU cc_start: 0.9090 (tt) cc_final: 0.8845 (tt) REVERT: J 96 ASP cc_start: 0.8681 (t0) cc_final: 0.8454 (t0) REVERT: J 100 ASP cc_start: 0.8251 (m-30) cc_final: 0.7590 (m-30) REVERT: J 100 TYR cc_start: 0.7773 (m-10) cc_final: 0.7273 (m-10) REVERT: N 42 TYR cc_start: 0.7111 (m-80) cc_final: 0.6286 (m-10) REVERT: N 66 ASN cc_start: 0.7783 (m-40) cc_final: 0.7389 (m-40) REVERT: N 97 GLU cc_start: 0.9183 (tp30) cc_final: 0.8797 (pm20) REVERT: j 95 MET cc_start: 0.8251 (ptm) cc_final: 0.7781 (ptt) REVERT: j 320 MET cc_start: 0.8165 (ptp) cc_final: 0.7829 (ptp) REVERT: k 530 MET cc_start: 0.8432 (mtm) cc_final: 0.7653 (mtm) REVERT: k 633 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8536 (mttm) REVERT: k 659 GLU cc_start: 0.8542 (tt0) cc_final: 0.8144 (tp30) outliers start: 63 outliers final: 40 residues processed: 185 average time/residue: 0.1492 time to fit residues: 43.8794 Evaluate side-chains 171 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain f residue 83 GLU Chi-restraints excluded: chain f residue 86 LEU Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 181 ILE Chi-restraints excluded: chain f residue 187 ASN Chi-restraints excluded: chain f residue 496 VAL Chi-restraints excluded: chain g residue 546 SER Chi-restraints excluded: chain g residue 603 ILE Chi-restraints excluded: chain g residue 633 LYS Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain M residue 11 MET Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain h residue 123 THR Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 187 ASN Chi-restraints excluded: chain h residue 496 VAL Chi-restraints excluded: chain i residue 520 ARG Chi-restraints excluded: chain i residue 545 LEU Chi-restraints excluded: chain i residue 546 SER Chi-restraints excluded: chain i residue 603 ILE Chi-restraints excluded: chain i residue 633 LYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain j residue 86 LEU Chi-restraints excluded: chain j residue 101 VAL Chi-restraints excluded: chain j residue 123 THR Chi-restraints excluded: chain j residue 127 VAL Chi-restraints excluded: chain j residue 187 ASN Chi-restraints excluded: chain j residue 297 ILE Chi-restraints excluded: chain j residue 427 TRP Chi-restraints excluded: chain j residue 477 ASP Chi-restraints excluded: chain j residue 496 VAL Chi-restraints excluded: chain j residue 499 THR Chi-restraints excluded: chain k residue 546 SER Chi-restraints excluded: chain k residue 603 ILE Chi-restraints excluded: chain k residue 633 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 209 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 152 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 230 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 40 optimal weight: 0.5980 chunk 200 optimal weight: 8.9990 chunk 30 optimal weight: 0.2980 chunk 91 optimal weight: 20.0000 chunk 182 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 ASN j 99 ASN k 616 ASN ** k 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.062985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.046258 restraints weight = 103195.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.047726 restraints weight = 54678.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.048672 restraints weight = 37906.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.049203 restraints weight = 30601.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.049208 restraints weight = 27228.968| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21528 Z= 0.127 Angle : 0.639 13.938 29472 Z= 0.302 Chirality : 0.046 0.273 3603 Planarity : 0.003 0.051 3498 Dihedral : 7.492 58.164 5334 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.06 % Allowed : 14.22 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.17), residues: 2382 helix: -0.00 (0.26), residues: 435 sheet: -0.49 (0.20), residues: 684 loop : -0.64 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 83 TYR 0.032 0.001 TYR N 87 PHE 0.010 0.001 PHE I 67 TRP 0.077 0.002 TRP N 107 HIS 0.002 0.001 HIS f 374 Details of bonding type rmsd covalent geometry : bond 0.00291 (21354) covalent geometry : angle 0.59159 (28992) SS BOND : bond 0.00238 ( 42) SS BOND : angle 0.64412 ( 84) hydrogen bonds : bond 0.03404 ( 670) hydrogen bonds : angle 5.15884 ( 2010) link_ALPHA1-3 : bond 0.00468 ( 6) link_ALPHA1-3 : angle 2.76216 ( 18) link_ALPHA1-6 : bond 0.00321 ( 6) link_ALPHA1-6 : angle 1.56725 ( 18) link_BETA1-4 : bond 0.00451 ( 51) link_BETA1-4 : angle 1.58279 ( 153) link_NAG-ASN : bond 0.00333 ( 69) link_NAG-ASN : angle 2.49819 ( 207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 135 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.7436 (mmm) cc_final: 0.6878 (mmm) REVERT: H 35 ASN cc_start: 0.8157 (t0) cc_final: 0.7576 (t0) REVERT: H 82 LEU cc_start: 0.9302 (pt) cc_final: 0.8963 (tt) REVERT: H 100 ASP cc_start: 0.7848 (m-30) cc_final: 0.7607 (m-30) REVERT: L 4 LEU cc_start: 0.8395 (mm) cc_final: 0.8066 (tp) REVERT: L 42 TYR cc_start: 0.7169 (m-80) cc_final: 0.6315 (m-10) REVERT: L 66 ASN cc_start: 0.7768 (m-40) cc_final: 0.7314 (m-40) REVERT: L 87 TYR cc_start: 0.7931 (m-80) cc_final: 0.6923 (m-10) REVERT: L 97 GLU cc_start: 0.9156 (tp30) cc_final: 0.8787 (pm20) REVERT: f 95 MET cc_start: 0.8190 (ptm) cc_final: 0.7735 (ptm) REVERT: f 320 MET cc_start: 0.8313 (ptp) cc_final: 0.7879 (ptp) REVERT: g 530 MET cc_start: 0.8560 (mtm) cc_final: 0.7793 (mtm) REVERT: g 633 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8435 (mttm) REVERT: g 659 GLU cc_start: 0.8638 (tt0) cc_final: 0.8133 (tp30) REVERT: I 34 MET cc_start: 0.8257 (mmt) cc_final: 0.7923 (tpt) REVERT: I 78 LEU cc_start: 0.9275 (tp) cc_final: 0.8947 (tt) REVERT: M 4 LEU cc_start: 0.8388 (mm) cc_final: 0.8009 (tp) REVERT: M 42 TYR cc_start: 0.7047 (m-80) cc_final: 0.6749 (m-10) REVERT: M 66 ASN cc_start: 0.7701 (m-40) cc_final: 0.7356 (m110) REVERT: M 87 TYR cc_start: 0.7811 (m-80) cc_final: 0.6844 (m-10) REVERT: M 97 GLU cc_start: 0.9105 (tp30) cc_final: 0.8764 (pm20) REVERT: h 95 MET cc_start: 0.8309 (ptm) cc_final: 0.7928 (ptt) REVERT: h 104 MET cc_start: 0.9294 (ttt) cc_final: 0.9020 (ttm) REVERT: h 320 MET cc_start: 0.8400 (ptp) cc_final: 0.7957 (ptp) REVERT: h 434 MET cc_start: 0.7722 (tmm) cc_final: 0.7454 (tmm) REVERT: i 530 MET cc_start: 0.8482 (mtm) cc_final: 0.7568 (mtm) REVERT: i 617 LYS cc_start: 0.9449 (mttp) cc_final: 0.9194 (mttt) REVERT: i 633 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8534 (mttm) REVERT: i 659 GLU cc_start: 0.8611 (tt0) cc_final: 0.8093 (tp30) REVERT: J 45 LEU cc_start: 0.8662 (tp) cc_final: 0.8327 (mm) REVERT: J 72 ASP cc_start: 0.8673 (m-30) cc_final: 0.8098 (t0) REVERT: J 75 LYS cc_start: 0.9650 (mptt) cc_final: 0.9178 (mtmm) REVERT: J 78 LEU cc_start: 0.9293 (tp) cc_final: 0.8866 (tt) REVERT: J 82 LEU cc_start: 0.9054 (tt) cc_final: 0.8821 (tt) REVERT: J 100 ASP cc_start: 0.8190 (m-30) cc_final: 0.7564 (m-30) REVERT: N 42 TYR cc_start: 0.6948 (m-80) cc_final: 0.6431 (m-10) REVERT: N 66 ASN cc_start: 0.7737 (m-40) cc_final: 0.7339 (m-40) REVERT: N 87 TYR cc_start: 0.7855 (m-80) cc_final: 0.6880 (m-10) REVERT: N 97 GLU cc_start: 0.9190 (tp30) cc_final: 0.8800 (pm20) REVERT: N 107 TRP cc_start: 0.7340 (p-90) cc_final: 0.7079 (p90) REVERT: j 95 MET cc_start: 0.8252 (ptm) cc_final: 0.7780 (ptt) REVERT: j 320 MET cc_start: 0.8128 (ptp) cc_final: 0.7755 (ptp) REVERT: k 530 MET cc_start: 0.8444 (mtm) cc_final: 0.7648 (mtm) REVERT: k 633 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8549 (mttm) REVERT: k 659 GLU cc_start: 0.8511 (tt0) cc_final: 0.8111 (tp30) outliers start: 65 outliers final: 49 residues processed: 190 average time/residue: 0.1547 time to fit residues: 46.1572 Evaluate side-chains 183 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 131 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 181 ILE Chi-restraints excluded: chain f residue 187 ASN Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain f residue 496 VAL Chi-restraints excluded: chain g residue 546 SER Chi-restraints excluded: chain g residue 593 LEU Chi-restraints excluded: chain g residue 603 ILE Chi-restraints excluded: chain g residue 633 LYS Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain M residue 11 MET Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain h residue 123 THR Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 187 ASN Chi-restraints excluded: chain h residue 488 VAL Chi-restraints excluded: chain h residue 496 VAL Chi-restraints excluded: chain i residue 520 ARG Chi-restraints excluded: chain i residue 545 LEU Chi-restraints excluded: chain i residue 546 SER Chi-restraints excluded: chain i residue 603 ILE Chi-restraints excluded: chain i residue 633 LYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 86 LEU Chi-restraints excluded: chain j residue 101 VAL Chi-restraints excluded: chain j residue 123 THR Chi-restraints excluded: chain j residue 125 LEU Chi-restraints excluded: chain j residue 126 CYS Chi-restraints excluded: chain j residue 127 VAL Chi-restraints excluded: chain j residue 187 ASN Chi-restraints excluded: chain j residue 297 ILE Chi-restraints excluded: chain j residue 427 TRP Chi-restraints excluded: chain j residue 477 ASP Chi-restraints excluded: chain j residue 488 VAL Chi-restraints excluded: chain j residue 494 LEU Chi-restraints excluded: chain j residue 496 VAL Chi-restraints excluded: chain k residue 545 LEU Chi-restraints excluded: chain k residue 546 SER Chi-restraints excluded: chain k residue 603 ILE Chi-restraints excluded: chain k residue 616 ASN Chi-restraints excluded: chain k residue 633 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 148 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 616 ASN k 616 ASN ** k 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.062678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.045977 restraints weight = 102969.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.047438 restraints weight = 54673.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.048368 restraints weight = 37957.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.048908 restraints weight = 30648.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.049233 restraints weight = 27205.202| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21528 Z= 0.169 Angle : 0.661 13.884 29472 Z= 0.313 Chirality : 0.046 0.272 3603 Planarity : 0.004 0.051 3498 Dihedral : 7.501 57.572 5334 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.06 % Allowed : 14.88 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.17), residues: 2382 helix: 0.12 (0.26), residues: 417 sheet: -0.42 (0.19), residues: 687 loop : -0.61 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG i 644 TYR 0.028 0.001 TYR N 87 PHE 0.008 0.001 PHE I 67 TRP 0.068 0.002 TRP M 107 HIS 0.003 0.001 HIS M 105 Details of bonding type rmsd covalent geometry : bond 0.00386 (21354) covalent geometry : angle 0.61516 (28992) SS BOND : bond 0.00253 ( 42) SS BOND : angle 0.64735 ( 84) hydrogen bonds : bond 0.03515 ( 670) hydrogen bonds : angle 5.12861 ( 2010) link_ALPHA1-3 : bond 0.00497 ( 6) link_ALPHA1-3 : angle 2.68238 ( 18) link_ALPHA1-6 : bond 0.00284 ( 6) link_ALPHA1-6 : angle 1.57149 ( 18) link_BETA1-4 : bond 0.00452 ( 51) link_BETA1-4 : angle 1.60002 ( 153) link_NAG-ASN : bond 0.00366 ( 69) link_NAG-ASN : angle 2.51777 ( 207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 129 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.7422 (mmm) cc_final: 0.6829 (mmm) REVERT: H 35 ASN cc_start: 0.8136 (t0) cc_final: 0.7517 (t0) REVERT: H 82 LEU cc_start: 0.9268 (pt) cc_final: 0.8925 (tt) REVERT: H 96 ASP cc_start: 0.8529 (t70) cc_final: 0.8328 (t0) REVERT: H 100 ASP cc_start: 0.7855 (m-30) cc_final: 0.7591 (m-30) REVERT: L 4 LEU cc_start: 0.8453 (mm) cc_final: 0.8167 (tp) REVERT: L 42 TYR cc_start: 0.7207 (m-80) cc_final: 0.6406 (m-10) REVERT: L 66 ASN cc_start: 0.7762 (m-40) cc_final: 0.7313 (m-40) REVERT: L 97 GLU cc_start: 0.9126 (tp30) cc_final: 0.8795 (pm20) REVERT: f 95 MET cc_start: 0.8204 (ptm) cc_final: 0.7732 (ptm) REVERT: f 104 MET cc_start: 0.9039 (ttm) cc_final: 0.8529 (tmm) REVERT: f 320 MET cc_start: 0.8302 (ptp) cc_final: 0.7892 (ptp) REVERT: g 530 MET cc_start: 0.8598 (mtm) cc_final: 0.7824 (mtm) REVERT: g 633 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8442 (mttm) REVERT: g 659 GLU cc_start: 0.8640 (tt0) cc_final: 0.8127 (tp30) REVERT: I 34 MET cc_start: 0.8260 (mmt) cc_final: 0.8047 (tpt) REVERT: I 78 LEU cc_start: 0.9271 (tp) cc_final: 0.8917 (tt) REVERT: M 4 LEU cc_start: 0.8448 (mm) cc_final: 0.8122 (tp) REVERT: M 42 TYR cc_start: 0.7091 (m-80) cc_final: 0.6748 (m-10) REVERT: M 66 ASN cc_start: 0.7717 (m-40) cc_final: 0.7346 (m110) REVERT: M 97 GLU cc_start: 0.9103 (tp30) cc_final: 0.8770 (pm20) REVERT: h 95 MET cc_start: 0.8321 (ptm) cc_final: 0.7909 (ptm) REVERT: h 104 MET cc_start: 0.9317 (ttt) cc_final: 0.9041 (ttm) REVERT: h 320 MET cc_start: 0.8406 (ptp) cc_final: 0.7982 (ptp) REVERT: h 434 MET cc_start: 0.7806 (tmm) cc_final: 0.7475 (tmm) REVERT: i 530 MET cc_start: 0.8485 (mtm) cc_final: 0.7433 (mtm) REVERT: i 633 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8550 (mttm) REVERT: i 659 GLU cc_start: 0.8677 (tt0) cc_final: 0.8072 (tp30) REVERT: J 45 LEU cc_start: 0.8671 (tp) cc_final: 0.8319 (mm) REVERT: J 72 ASP cc_start: 0.8660 (m-30) cc_final: 0.8073 (t0) REVERT: J 75 LYS cc_start: 0.9652 (mptt) cc_final: 0.9184 (mtmm) REVERT: J 78 LEU cc_start: 0.9239 (tp) cc_final: 0.8901 (tt) REVERT: J 82 LEU cc_start: 0.8958 (tt) cc_final: 0.8712 (tt) REVERT: N 42 TYR cc_start: 0.7023 (m-80) cc_final: 0.6394 (m-10) REVERT: N 66 ASN cc_start: 0.7786 (m-40) cc_final: 0.7364 (m-40) REVERT: N 97 GLU cc_start: 0.9177 (tp30) cc_final: 0.8820 (pm20) REVERT: N 107 TRP cc_start: 0.7403 (p-90) cc_final: 0.7170 (p90) REVERT: j 320 MET cc_start: 0.8145 (ptp) cc_final: 0.7781 (ptp) REVERT: k 530 MET cc_start: 0.8445 (mtm) cc_final: 0.7634 (mtm) REVERT: k 659 GLU cc_start: 0.8512 (tt0) cc_final: 0.8098 (tp30) outliers start: 65 outliers final: 50 residues processed: 185 average time/residue: 0.1432 time to fit residues: 42.4675 Evaluate side-chains 181 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 129 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 181 ILE Chi-restraints excluded: chain f residue 187 ASN Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain f residue 496 VAL Chi-restraints excluded: chain g residue 546 SER Chi-restraints excluded: chain g residue 593 LEU Chi-restraints excluded: chain g residue 603 ILE Chi-restraints excluded: chain g residue 633 LYS Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain h residue 123 THR Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 187 ASN Chi-restraints excluded: chain h residue 488 VAL Chi-restraints excluded: chain h residue 496 VAL Chi-restraints excluded: chain i residue 520 ARG Chi-restraints excluded: chain i residue 545 LEU Chi-restraints excluded: chain i residue 546 SER Chi-restraints excluded: chain i residue 603 ILE Chi-restraints excluded: chain i residue 616 ASN Chi-restraints excluded: chain i residue 633 LYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 86 LEU Chi-restraints excluded: chain j residue 101 VAL Chi-restraints excluded: chain j residue 123 THR Chi-restraints excluded: chain j residue 125 LEU Chi-restraints excluded: chain j residue 126 CYS Chi-restraints excluded: chain j residue 127 VAL Chi-restraints excluded: chain j residue 187 ASN Chi-restraints excluded: chain j residue 297 ILE Chi-restraints excluded: chain j residue 427 TRP Chi-restraints excluded: chain j residue 477 ASP Chi-restraints excluded: chain j residue 488 VAL Chi-restraints excluded: chain j residue 496 VAL Chi-restraints excluded: chain k residue 545 LEU Chi-restraints excluded: chain k residue 546 SER Chi-restraints excluded: chain k residue 603 ILE Chi-restraints excluded: chain k residue 633 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 10 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 206 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 199 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 114 GLN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 616 ASN ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.061408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.044674 restraints weight = 104099.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.046115 restraints weight = 55638.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.046996 restraints weight = 38793.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.047535 restraints weight = 31676.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.047848 restraints weight = 27976.901| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 21528 Z= 0.298 Angle : 0.785 13.602 29472 Z= 0.374 Chirality : 0.048 0.258 3603 Planarity : 0.004 0.055 3498 Dihedral : 7.895 58.061 5334 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.97 % Allowed : 15.40 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.17), residues: 2382 helix: -0.05 (0.26), residues: 399 sheet: -0.54 (0.19), residues: 714 loop : -0.77 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 66 TYR 0.035 0.002 TYR N 87 PHE 0.013 0.002 PHE i 522 TRP 0.070 0.002 TRP L 107 HIS 0.008 0.002 HIS M 105 Details of bonding type rmsd covalent geometry : bond 0.00660 (21354) covalent geometry : angle 0.74040 (28992) SS BOND : bond 0.00366 ( 42) SS BOND : angle 0.90616 ( 84) hydrogen bonds : bond 0.04101 ( 670) hydrogen bonds : angle 5.43782 ( 2010) link_ALPHA1-3 : bond 0.00635 ( 6) link_ALPHA1-3 : angle 2.48882 ( 18) link_ALPHA1-6 : bond 0.00200 ( 6) link_ALPHA1-6 : angle 1.64964 ( 18) link_BETA1-4 : bond 0.00492 ( 51) link_BETA1-4 : angle 1.81566 ( 153) link_NAG-ASN : bond 0.00589 ( 69) link_NAG-ASN : angle 2.70186 ( 207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 122 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 ASN cc_start: 0.8044 (t0) cc_final: 0.7485 (t0) REVERT: H 82 LEU cc_start: 0.9310 (pt) cc_final: 0.9002 (tt) REVERT: L 42 TYR cc_start: 0.7361 (m-80) cc_final: 0.6532 (m-10) REVERT: L 66 ASN cc_start: 0.7698 (m-40) cc_final: 0.7238 (m-40) REVERT: L 87 TYR cc_start: 0.7944 (m-80) cc_final: 0.6937 (m-10) REVERT: L 97 GLU cc_start: 0.9152 (tp30) cc_final: 0.8795 (pm20) REVERT: f 426 MET cc_start: 0.8155 (ptm) cc_final: 0.7950 (tmm) REVERT: g 530 MET cc_start: 0.8746 (mtm) cc_final: 0.7973 (mtm) REVERT: g 589 ASP cc_start: 0.9085 (m-30) cc_final: 0.8868 (m-30) REVERT: g 633 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8556 (mttm) REVERT: g 659 GLU cc_start: 0.8689 (tt0) cc_final: 0.8079 (tp30) REVERT: I 34 MET cc_start: 0.8282 (mmt) cc_final: 0.8051 (tpt) REVERT: I 78 LEU cc_start: 0.9285 (tp) cc_final: 0.8926 (tt) REVERT: M 4 LEU cc_start: 0.8535 (mm) cc_final: 0.8080 (tp) REVERT: M 42 TYR cc_start: 0.7338 (m-80) cc_final: 0.6572 (m-10) REVERT: M 66 ASN cc_start: 0.7761 (m-40) cc_final: 0.7377 (m110) REVERT: M 87 TYR cc_start: 0.7883 (m-80) cc_final: 0.6906 (m-10) REVERT: M 97 GLU cc_start: 0.9137 (tp30) cc_final: 0.8813 (pm20) REVERT: h 95 MET cc_start: 0.8314 (ptm) cc_final: 0.7949 (ptm) REVERT: h 104 MET cc_start: 0.9381 (ttt) cc_final: 0.9111 (ttm) REVERT: h 320 MET cc_start: 0.8500 (ptp) cc_final: 0.8282 (ptp) REVERT: i 530 MET cc_start: 0.8533 (mtm) cc_final: 0.7410 (mtm) REVERT: i 659 GLU cc_start: 0.8823 (tt0) cc_final: 0.8068 (tp30) REVERT: J 34 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.8003 (tpt) REVERT: J 45 LEU cc_start: 0.8757 (tp) cc_final: 0.8337 (mm) REVERT: J 72 ASP cc_start: 0.8725 (m-30) cc_final: 0.8119 (t0) REVERT: J 75 LYS cc_start: 0.9663 (mptt) cc_final: 0.9206 (mtmm) REVERT: J 78 LEU cc_start: 0.9281 (tp) cc_final: 0.9076 (tp) REVERT: J 82 LEU cc_start: 0.9073 (tt) cc_final: 0.8837 (tt) REVERT: J 102 TYR cc_start: 0.8030 (m-80) cc_final: 0.7794 (m-80) REVERT: N 42 TYR cc_start: 0.7196 (m-80) cc_final: 0.6437 (m-10) REVERT: N 66 ASN cc_start: 0.7765 (m-40) cc_final: 0.7354 (m110) REVERT: N 87 TYR cc_start: 0.7938 (m-80) cc_final: 0.6954 (m-10) REVERT: N 97 GLU cc_start: 0.9194 (tp30) cc_final: 0.8826 (pm20) REVERT: j 320 MET cc_start: 0.8261 (ptp) cc_final: 0.7823 (ptp) REVERT: k 530 MET cc_start: 0.8531 (mtm) cc_final: 0.7722 (mtm) REVERT: k 659 GLU cc_start: 0.8589 (tt0) cc_final: 0.8065 (tp30) outliers start: 63 outliers final: 51 residues processed: 178 average time/residue: 0.1443 time to fit residues: 41.4596 Evaluate side-chains 169 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 116 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 181 ILE Chi-restraints excluded: chain f residue 187 ASN Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain f residue 496 VAL Chi-restraints excluded: chain g residue 546 SER Chi-restraints excluded: chain g residue 593 LEU Chi-restraints excluded: chain g residue 603 ILE Chi-restraints excluded: chain g residue 633 LYS Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain h residue 120 VAL Chi-restraints excluded: chain h residue 123 THR Chi-restraints excluded: chain h residue 125 LEU Chi-restraints excluded: chain h residue 126 CYS Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 187 ASN Chi-restraints excluded: chain h residue 488 VAL Chi-restraints excluded: chain h residue 496 VAL Chi-restraints excluded: chain i residue 545 LEU Chi-restraints excluded: chain i residue 546 SER Chi-restraints excluded: chain i residue 603 ILE Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 86 LEU Chi-restraints excluded: chain j residue 101 VAL Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 123 THR Chi-restraints excluded: chain j residue 125 LEU Chi-restraints excluded: chain j residue 126 CYS Chi-restraints excluded: chain j residue 127 VAL Chi-restraints excluded: chain j residue 187 ASN Chi-restraints excluded: chain j residue 297 ILE Chi-restraints excluded: chain j residue 427 TRP Chi-restraints excluded: chain j residue 477 ASP Chi-restraints excluded: chain j residue 488 VAL Chi-restraints excluded: chain j residue 496 VAL Chi-restraints excluded: chain k residue 546 SER Chi-restraints excluded: chain k residue 603 ILE Chi-restraints excluded: chain k residue 633 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 20 optimal weight: 40.0000 chunk 96 optimal weight: 0.0770 chunk 205 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 229 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 176 optimal weight: 0.6980 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 652 GLN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.063509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.046981 restraints weight = 100379.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.048490 restraints weight = 53107.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.049294 restraints weight = 36602.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.049921 restraints weight = 30239.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.050273 restraints weight = 26193.868| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21528 Z= 0.114 Angle : 0.662 13.718 29472 Z= 0.313 Chirality : 0.046 0.263 3603 Planarity : 0.003 0.055 3498 Dihedral : 7.558 59.816 5334 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.07 % Allowed : 16.24 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.17), residues: 2382 helix: 0.06 (0.26), residues: 420 sheet: -0.51 (0.19), residues: 735 loop : -0.49 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 83 TYR 0.028 0.001 TYR N 87 PHE 0.012 0.001 PHE H 100C TRP 0.086 0.002 TRP L 107 HIS 0.004 0.001 HIS N 105 Details of bonding type rmsd covalent geometry : bond 0.00261 (21354) covalent geometry : angle 0.61945 (28992) SS BOND : bond 0.00249 ( 42) SS BOND : angle 0.66925 ( 84) hydrogen bonds : bond 0.03381 ( 670) hydrogen bonds : angle 5.12064 ( 2010) link_ALPHA1-3 : bond 0.00447 ( 6) link_ALPHA1-3 : angle 2.74956 ( 18) link_ALPHA1-6 : bond 0.00431 ( 6) link_ALPHA1-6 : angle 1.47925 ( 18) link_BETA1-4 : bond 0.00432 ( 51) link_BETA1-4 : angle 1.47705 ( 153) link_NAG-ASN : bond 0.00312 ( 69) link_NAG-ASN : angle 2.45838 ( 207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.7469 (mmm) cc_final: 0.6736 (mmm) REVERT: H 35 ASN cc_start: 0.8155 (t0) cc_final: 0.7449 (t0) REVERT: H 82 LEU cc_start: 0.9285 (pt) cc_final: 0.8972 (tt) REVERT: L 42 TYR cc_start: 0.7137 (m-80) cc_final: 0.6282 (m-10) REVERT: L 66 ASN cc_start: 0.7676 (m-40) cc_final: 0.7210 (m-40) REVERT: L 97 GLU cc_start: 0.9103 (tp30) cc_final: 0.8793 (pm20) REVERT: f 104 MET cc_start: 0.9036 (ttm) cc_final: 0.8586 (tmm) REVERT: g 530 MET cc_start: 0.8548 (mtm) cc_final: 0.7744 (mtm) REVERT: g 589 ASP cc_start: 0.8964 (m-30) cc_final: 0.8755 (m-30) REVERT: g 633 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8470 (mttm) REVERT: g 659 GLU cc_start: 0.8621 (tt0) cc_final: 0.8066 (tp30) REVERT: I 34 MET cc_start: 0.8356 (mmt) cc_final: 0.8009 (tpt) REVERT: I 78 LEU cc_start: 0.9231 (tp) cc_final: 0.8881 (tt) REVERT: M 4 LEU cc_start: 0.8457 (mm) cc_final: 0.8118 (tp) REVERT: M 42 TYR cc_start: 0.7102 (m-80) cc_final: 0.6448 (m-10) REVERT: M 66 ASN cc_start: 0.7658 (m-40) cc_final: 0.7178 (m110) REVERT: M 97 GLU cc_start: 0.9095 (tp30) cc_final: 0.8789 (pm20) REVERT: h 95 MET cc_start: 0.8271 (ptm) cc_final: 0.7871 (ptm) REVERT: h 104 MET cc_start: 0.9309 (ttt) cc_final: 0.9034 (ttm) REVERT: h 434 MET cc_start: 0.7856 (tmm) cc_final: 0.7531 (tmm) REVERT: i 530 MET cc_start: 0.8395 (mtm) cc_final: 0.7341 (mtm) REVERT: i 659 GLU cc_start: 0.8671 (tt0) cc_final: 0.8033 (tp30) REVERT: J 34 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7707 (tpt) REVERT: J 45 LEU cc_start: 0.8803 (tp) cc_final: 0.8434 (mm) REVERT: J 72 ASP cc_start: 0.8641 (m-30) cc_final: 0.8043 (t0) REVERT: J 75 LYS cc_start: 0.9641 (mptt) cc_final: 0.9168 (mtmm) REVERT: J 82 MET cc_start: 0.8970 (mmm) cc_final: 0.8653 (mmm) REVERT: J 82 LEU cc_start: 0.9036 (tt) cc_final: 0.8798 (tt) REVERT: J 83 ARG cc_start: 0.9241 (mtm-85) cc_final: 0.8999 (ptt-90) REVERT: N 42 TYR cc_start: 0.6935 (m-80) cc_final: 0.6380 (m-10) REVERT: N 97 GLU cc_start: 0.9115 (tp30) cc_final: 0.8775 (pm20) REVERT: j 95 MET cc_start: 0.7966 (ptm) cc_final: 0.7475 (ppp) REVERT: j 104 MET cc_start: 0.9067 (ttm) cc_final: 0.8562 (tmm) REVERT: j 320 MET cc_start: 0.8019 (ptp) cc_final: 0.7668 (ptp) REVERT: k 530 MET cc_start: 0.8433 (mtm) cc_final: 0.7628 (mtm) REVERT: k 626 MET cc_start: 0.8745 (ttt) cc_final: 0.8544 (tmm) REVERT: k 659 GLU cc_start: 0.8529 (tt0) cc_final: 0.8057 (tp30) outliers start: 44 outliers final: 38 residues processed: 170 average time/residue: 0.1430 time to fit residues: 38.6901 Evaluate side-chains 166 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 181 ILE Chi-restraints excluded: chain f residue 187 ASN Chi-restraints excluded: chain f residue 496 VAL Chi-restraints excluded: chain g residue 593 LEU Chi-restraints excluded: chain g residue 603 ILE Chi-restraints excluded: chain g residue 633 LYS Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain h residue 120 VAL Chi-restraints excluded: chain h residue 488 VAL Chi-restraints excluded: chain h residue 496 VAL Chi-restraints excluded: chain i residue 520 ARG Chi-restraints excluded: chain i residue 545 LEU Chi-restraints excluded: chain i residue 603 ILE Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain j residue 86 LEU Chi-restraints excluded: chain j residue 101 VAL Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 123 THR Chi-restraints excluded: chain j residue 125 LEU Chi-restraints excluded: chain j residue 187 ASN Chi-restraints excluded: chain j residue 297 ILE Chi-restraints excluded: chain j residue 427 TRP Chi-restraints excluded: chain j residue 477 ASP Chi-restraints excluded: chain j residue 488 VAL Chi-restraints excluded: chain j residue 494 LEU Chi-restraints excluded: chain j residue 496 VAL Chi-restraints excluded: chain k residue 603 ILE Chi-restraints excluded: chain k residue 633 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 174 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 196 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 chunk 181 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 50 optimal weight: 0.2980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 422 GLN g 616 ASN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.063493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.046882 restraints weight = 100871.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.048382 restraints weight = 53243.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.049332 restraints weight = 36642.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.049884 restraints weight = 29535.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.050207 restraints weight = 26033.420| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21528 Z= 0.132 Angle : 0.660 13.743 29472 Z= 0.312 Chirality : 0.046 0.270 3603 Planarity : 0.003 0.056 3498 Dihedral : 7.434 57.184 5334 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.21 % Allowed : 16.05 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.17), residues: 2382 helix: 0.18 (0.27), residues: 417 sheet: -0.46 (0.19), residues: 735 loop : -0.48 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 83 TYR 0.031 0.001 TYR N 87 PHE 0.010 0.001 PHE j 382 TRP 0.092 0.002 TRP L 107 HIS 0.004 0.001 HIS M 105 Details of bonding type rmsd covalent geometry : bond 0.00302 (21354) covalent geometry : angle 0.61683 (28992) SS BOND : bond 0.00236 ( 42) SS BOND : angle 0.66559 ( 84) hydrogen bonds : bond 0.03386 ( 670) hydrogen bonds : angle 5.05824 ( 2010) link_ALPHA1-3 : bond 0.00494 ( 6) link_ALPHA1-3 : angle 2.52486 ( 18) link_ALPHA1-6 : bond 0.00363 ( 6) link_ALPHA1-6 : angle 1.53257 ( 18) link_BETA1-4 : bond 0.00445 ( 51) link_BETA1-4 : angle 1.50415 ( 153) link_NAG-ASN : bond 0.00339 ( 69) link_NAG-ASN : angle 2.46929 ( 207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3670.83 seconds wall clock time: 64 minutes 48.77 seconds (3888.77 seconds total)